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This page was generated on 2025-09-11 11:39 -0400 (Thu, 11 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4606
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4547
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: 2025-09-08 13:40 -0400 (Mon, 08 Sep 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 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for biodbChebi on kjohnson1

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: 2025-09-09 13:52:36 -0400 (Tue, 09 Sep 2025)
EndedAt: 2025-09-09 13:55:00 -0400 (Tue, 09 Sep 2025)
EllapsedTime: 143.7 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 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* 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
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
ChebiConn 2.612  1.111   5.259
* 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 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
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 [2025-09-09 13:53:29.358][biodb::testContext]
biodb.INFO [2025-09-09 13:53:29.363][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-09 13:53:29.365][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-09-09 13:53:29.366][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-09 13:53:29.366][biodb::testContext]
biodb.INFO [2025-09-09 13:53:29.375][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-09-09 13:53:29.377][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-09-09 13:53:29.386][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-09 13:53:29.387][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-09 13:53:29.388][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-09 13:53:29.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.392][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-09 13:53:29.410][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-09 13:53:29.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.414][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-09 13:53:29.415][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-09 13:53:29.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.419][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-09 13:53:29.421][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-09 13:53:29.422][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-09 13:53:29.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.426][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-09 13:53:29.427][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-09 13:53:29.428][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-09 13:53:29.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.431][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-09 13:53:29.432][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-09 13:53:29.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.435][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-09 13:53:29.436][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-09 13:53:29.436][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-09 13:53:29.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.441][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-09 13:53:29.443][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-09 13:53:29.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.445][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[2025-09-09 13:53:29.446][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-09 13:53:29.447][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-09 13:53:29.448][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-09 13:53:29.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.451][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-09 13:53:29.452][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-09 13:53:29.453][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-09 13:53:29.453][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-09 13:53:29.454][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-09 13:53:29.455][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-09 13:53:29.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.457][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[2025-09-09 13:53:29.459][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-09 13:53:29.460][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-09 13:53:29.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.465][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-09 13:53:29.466][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-09 13:53:29.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.469][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-09 13:53:29.470][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-09 13:53:29.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.473][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-09 13:53:29.474][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-09-09 13:53:29.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.477][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-09 13:53:29.478][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-09 13:53:29.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.481][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-09 13:53:29.482][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-09 13:53:29.504][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-09 13:53:29.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.508][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-09 13:53:29.509][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-09 13:53:29.510][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-09 13:53:29.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.516][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-09 13:53:29.553][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-09 13:53:29.578][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-09-09 13:53:29.579][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-09 13:53:29.580][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-09 13:53:29.582][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-09 13:53:29.583][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-09 13:53:29.584][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-09 13:53:29.585][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-09 13:53:29.586][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-09 13:53:29.587][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-09 13:53:29.588][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-09 13:53:29.589][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-09 13:53:29.590][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-09 13:53:29.590][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-09 13:53:29.591][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-09 13:53:29.592][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-09 13:53:29.592][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-09 13:53:29.592][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-09 13:53:29.592][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-09 13:53:29.592][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-09 13:53:29.593][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-09 13:53:29.594][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:53:29.595][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:53:29.596][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-09 13:53:29.596][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:53:29.597][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:53:29.598][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-09 13:53:29.599][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-09 13:53:29.600][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-09 13:53:29.600][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-09 13:53:29.601][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-09 13:53:29.602][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-09 13:53:29.603][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-09 13:53:29.605][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-09 13:53:29.606][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-09 13:53:29.606][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-09 13:53:29.607][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-09 13:53:29.610][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-09 13:53:29.611][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-09 13:53:29.612][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-09 13:53:29.614][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-09 13:53:29.615][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-09 13:53:29.616][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-09 13:53:29.617][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-09 13:53:29.618][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-09 13:53:29.619][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-09 13:53:29.621][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-09 13:53:29.622][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-09 13:53:29.623][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-09 13:53:29.623][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-09 13:53:29.623][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-09 13:53:29.623][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-09 13:53:29.623][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-09 13:53:29.624][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-09 13:53:29.626][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:53:29.627][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:53:29.628][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-09 13:53:29.628][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:53:29.629][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:53:29.630][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-09 13:53:29.631][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-09 13:53:29.632][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-09 13:53:29.632][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-09 13:53:29.633][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-09 13:53:29.634][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-09 13:53:29.635][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-09 13:53:29.637][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-09 13:53:29.638][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-09-09 13:53:29.639][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-09 13:53:29.640][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-09 13:53:29.641][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-09 13:53:29.641][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-09 13:53:29.642][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-09 13:53:29.643][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-09 13:53:29.644][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-09 13:53:29.645][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-09 13:53:29.646][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-09 13:53:29.646][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-09 13:53:29.647][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-09 13:53:29.648][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-09 13:53:29.649][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-09 13:53:29.650][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-09 13:53:29.651][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-09 13:53:29.651][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:53:29.652][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:53:29.653][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-09 13:53:29.654][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:53:29.655][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:53:29.655][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-09 13:53:29.656][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-09 13:53:29.657][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-09 13:53:29.658][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-09 13:53:29.658][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-09 13:53:29.659][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-09 13:53:29.660][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-09 13:53:29.663][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-09 13:53:29.664][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-09 13:53:29.666][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-09 13:53:29.667][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-09 13:53:29.668][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-09 13:53:29.668][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-09 13:53:29.669][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-09 13:53:29.670][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-09 13:53:29.671][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-09 13:53:29.672][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-09 13:53:29.673][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-09 13:53:29.674][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-09 13:53:29.674][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-09 13:53:29.675][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-09 13:53:29.676][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-09 13:53:29.677][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-09 13:53:29.678][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-09 13:53:29.679][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:53:29.679][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:53:29.680][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-09 13:53:29.681][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:53:29.682][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:53:29.682][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-09 13:53:29.683][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-09 13:53:29.684][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-09 13:53:29.685][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-09 13:53:29.686][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-09 13:53:29.686][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-09 13:53:29.691][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-09 13:53:29.692][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.726][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[2025-09-09 13:53:29.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.741][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[2025-09-09 13:53:29.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.749][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[2025-09-09 13:53:29.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.752][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[2025-09-09 13:53:29.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.768][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-09 13:53:29.773][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-09 13:53:29.775][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-09 13:53:29.776][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-09 13:53:29.778][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-09 13:53:29.779][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-09 13:53:29.780][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-09 13:53:29.781][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-09 13:53:29.783][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-09 13:53:29.784][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-09 13:53:29.785][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-09 13:53:29.786][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-09 13:53:29.787][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-09 13:53:29.789][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-09 13:53:29.790][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-09 13:53:29.791][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-09 13:53:29.792][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-09 13:53:29.793][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-09 13:53:29.794][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-09 13:53:29.796][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-09 13:53:29.797][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-09 13:53:29.798][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-09 13:53:29.799][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-09 13:53:29.800][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-09 13:53:29.802][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-09 13:53:29.803][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-09 13:53:29.804][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-09 13:53:29.805][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-09 13:53:29.806][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-09 13:53:29.808][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-09 13:53:29.810][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-09 13:53:29.812][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-09 13:53:29.814][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-09 13:53:29.815][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-09 13:53:29.816][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-09 13:53:29.817][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-09 13:53:29.819][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-09 13:53:29.820][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-09 13:53:29.821][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-09 13:53:29.822][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-09 13:53:29.823][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-09 13:53:29.825][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-09 13:53:29.826][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-09 13:53:29.828][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-09 13:53:29.831][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-09 13:53:29.833][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-09 13:53:29.834][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-09 13:53:29.835][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-09 13:53:29.837][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-09 13:53:29.838][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-09 13:53:29.839][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-09 13:53:29.840][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-09 13:53:29.841][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-09 13:53:29.843][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-09 13:53:29.844][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-09 13:53:29.845][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-09 13:53:29.846][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-09 13:53:29.847][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-09 13:53:29.849][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-09 13:53:29.850][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-09 13:53:29.851][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-09 13:53:29.853][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-09 13:53:29.854][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-09 13:53:29.855][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-09 13:53:29.857][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-09 13:53:29.858][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-09 13:53:29.859][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-09 13:53:29.860][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-09 13:53:29.862][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-09 13:53:29.864][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-09 13:53:29.866][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-09 13:53:29.868][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-09 13:53:29.869][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-09 13:53:29.871][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-09 13:53:29.872][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-09 13:53:29.873][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-09 13:53:29.875][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-09 13:53:29.876][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-09 13:53:29.877][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-09 13:53:29.879][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-09 13:53:29.880][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-09 13:53:29.881][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-09 13:53:29.883][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-09 13:53:29.889][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-09 13:53:29.891][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-09-09 13:53:29.894][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-09 13:53:29.895][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.897][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:29.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:29.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.917][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[2025-09-09 13:53:29.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:29.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:29.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:29.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:29.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.928][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[2025-09-09 13:53:29.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:29.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:29.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.933][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.DEBUG[2025-09-09 13:53:29.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:29.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:29.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:29.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:29.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.944][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[2025-09-09 13:53:29.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:29.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:29.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:29.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:29.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:29.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:29.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.962][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.DEBUG[2025-09-09 13:53:29.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:29.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:29.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:29.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:29.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:29.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:29.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:29.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:29.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.983][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[2025-09-09 13:53:29.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:29.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:29.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:29.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:29.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:29.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.993][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[2025-09-09 13:53:29.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:29.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:29.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:29.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:29.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:29.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:29.999][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[2025-09-09 13:53:29.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:53:30.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:30.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:30.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:30.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:30.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:30.004][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[2025-09-09 13:53:30.007][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-09-09 13:53:30.018][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-09-09 13:53:30.020][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-09 13:53:30.021][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-09-09 13:53:30.022][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-09 13:53:30.023][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-09 13:53:30.024][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-09 13:53:30.024][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-09 13:53:30.025][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-09 13:53:30.026][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-09-09 13:53:30.027][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-09 13:53:30.028][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-09 13:53:30.029][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-09 13:53:30.030][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-09-09 13:53:30.030][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-09 13:53:30.031][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-09-09 13:53:30.031][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-09-09 13:53:30.031][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-09-09 13:53:30.031][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-09-09 13:53:30.031][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-09-09 13:53:30.031][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-09-09 13:53:30.031][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-09-09 13:53:30.031][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-09-09 13:53:30.031][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-09-09 13:53:30.031][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-09-09 13:53:30.031][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-09-09 13:53:30.032][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-09 13:53:30.033][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-09 13:53:30.033][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-09 13:53:30.033][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-09 13:53:30.034][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-09 13:53:30.035][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:53:30.036][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:53:30.037][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-09 13:53:30.038][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:53:30.039][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:53:30.039][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-09 13:53:30.040][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:53:30.040][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-09-09 13:53:30.041][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-09 13:53:30.042][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-09 13:53:30.043][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-09 13:53:30.044][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-09-09 13:53:30.044][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-09-09 13:53:30.050][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-09 13:53:30.052][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-09 13:53:30.053][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-09-09 13:53:30.055][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-09 13:53:30.057][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-09 13:53:30.058][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-09 13:53:30.134][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-09-09 13:53:30.136][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-09-09 13:53:30.141][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-09-09 13:53:30.146][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-09-09 13:53:30.151][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-09-09 13:53:30.152][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-09-09 13:53:30.154][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-09-09 13:53:30.155][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-09-09 13:53:30.167][biodb::testThat]
biodb.INFO [2025-09-09 13:53:30.169][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-09-09 13:53:30.171][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:53:30.171][biodb::testThat]
biodb.TRACE[2025-09-09 13:53:30.179][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[2025-09-09 13:53:30.181][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:53:30.185][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:53:30.194][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:53:30.195][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:30.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:30.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:30.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:30.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:30.220][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.TRACE[2025-09-09 13:53:30.231][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:30.233][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:30.233][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.234][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:30.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:30.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.255][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:53:30.257][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:53:30.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.258][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.286][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:53:30.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:53:30.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.290][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:53:30.291][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:53:30.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.292][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.294][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:53:30.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:53:30.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.297][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:53:30.298][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:53:30.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.300][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.301][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:53:30.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:53:30.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.304][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:53:30.305][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:53:30.306][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.307][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.308][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:53:30.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:53:30.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.312][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:53:30.313][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:53:30.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.316][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.318][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:53:30.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:53:30.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.324][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:53:30.325][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:30.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.327][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.328][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:53:30.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:30.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.333][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:30.334][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:30.335][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.336][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:30.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:30.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.352][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:30.353][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:30.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.355][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.356][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:30.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:30.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.360][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:53:30.361][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:53:30.362][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.362][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.364][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:53:30.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:53:30.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.367][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:53:30.369][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:53:30.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.372][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.373][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:53:30.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:53:30.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:30.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:30.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:30.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:30.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:30.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:30.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:30.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:30.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:30.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:30.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:30.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:30.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:30.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:30.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:53:30.448][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-09-09 13:53:30.451][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:53:30.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:53:30.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.455][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:53:30.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:53:30.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:53:30.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:53:30.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.499][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:53:30.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:53:30.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.503][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:30.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:30.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:30.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:30.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.510][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-09 13:53:30.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-09 13:53:30.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.513][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-09 13:53:30.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-09 13:53:30.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.517][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-09 13:53:30.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-09 13:53:30.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.520][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-09 13:53:30.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-09 13:53:30.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:30.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:30.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:30.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:30.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:30.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:30.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:30.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:30.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:30.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:30.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:30.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:30.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:30.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:30.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:30.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:30.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:30.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:30.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:30.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:30.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.634][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:30.635][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:30.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.637][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:30.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:30.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.667][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.670][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.674][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.675][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.676][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:53:30.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.689][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:30.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:30.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.694][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:30.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:30.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.699][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:30.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:30.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.703][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:30.704][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:30.705][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.706][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.707][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:30.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:30.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.721][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:53:30.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:53:30.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.725][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:53:30.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:53:30.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.729][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:53:30.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:53:30.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.732][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:53:30.733][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:53:30.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.734][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.735][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:53:30.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:53:30.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.752][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:30.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:30.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.756][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:30.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:30.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.761][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:30.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:30.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.766][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:30.768][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:30.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.769][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:30.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:30.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:30.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:30.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:30.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:30.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:30.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:30.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.802][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:30.803][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:30.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.804][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:30.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:30.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.819][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:53:30.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:53:30.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.832][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:53:30.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:53:30.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.837][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:53:30.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:53:30.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.841][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:53:30.841][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:53:30.842][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.843][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.844][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:53:30.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:53:30.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.856][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-09-09 13:53:30.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:53:30.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.861][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-09-09 13:53:30.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:53:30.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.866][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-09-09 13:53:30.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:53:30.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.870][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-09-09 13:53:30.871][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:53:30.872][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.873][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.874][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-09-09 13:53:30.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:53:30.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.886][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:53:30.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:53:30.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.890][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:53:30.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:53:30.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.893][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:53:30.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:53:30.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.897][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:53:30.898][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:53:30.899][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.900][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.900][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:53:30.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:53:30.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.913][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:53:30.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:53:30.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.917][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:53:30.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:53:30.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.920][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:53:30.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:53:30.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.925][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:53:30.927][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:53:30.929][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.930][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.931][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:53:30.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:53:30.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.943][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:53:30.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:53:30.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.947][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:53:30.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:53:30.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.951][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:53:30.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:53:30.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.954][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:53:30.955][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:53:30.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.956][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.957][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:53:30.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:53:30.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.969][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:53:30.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:53:30.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.973][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:53:30.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:53:30.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.976][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:53:30.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:53:30.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.986][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:53:30.987][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:53:30.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.989][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:30.989][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:53:30.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:53:30.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:30.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.003][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:31.004][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:31.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.006][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.011][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:53:31.012][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:53:31.014][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.015][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.021][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:53:31.022][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:53:31.023][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.024][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.029][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:53:31.030][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:53:31.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.032][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.037][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:53:31.038][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:53:31.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.039][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.045][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:53:31.047][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:53:31.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.049][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.056][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:31.057][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:31.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.059][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.065][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:31.066][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:31.067][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.067][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.072][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-09-09 13:53:31.073][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:53:31.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.075][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.080][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:31.081][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:31.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.083][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.088][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:53:31.089][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:53:31.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.091][ef$get] fields variable is a list.
biodb.INFO [2025-09-09 13:53:31.100][biodb::testThat]
biodb.INFO [2025-09-09 13:53:31.101][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-09-09 13:53:31.102][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:53:31.103][biodb::testThat]
biodb.DEBUG[2025-09-09 13:53:31.117][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-09-09 13:53:31.126][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:53:31.130][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-09-09 13:53:31.132][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:53:31.133][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-09-09 13:53:31.134][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:53:31.166][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:53:31.168][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:53:31.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:53:31.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:31.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:31.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:31.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:31.179][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:31.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:53:31.183][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:31.184][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:31.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.185][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:31.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:31.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.207][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:53:31.208][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:53:31.209][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.210][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.211][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:53:31.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:53:31.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.215][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:53:31.216][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:53:31.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.217][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.218][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:53:31.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:53:31.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.222][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:53:31.223][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:53:31.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.224][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.225][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:53:31.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:53:31.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.229][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:53:31.230][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:53:31.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.231][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.232][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:53:31.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:53:31.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.236][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:53:31.236][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:53:31.237][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.238][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.239][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:53:31.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:53:31.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.244][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:53:31.245][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:31.246][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.246][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.248][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:53:31.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:31.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.251][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:31.252][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:31.253][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.254][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:31.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:31.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.258][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:31.259][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:31.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.261][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.262][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:31.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:31.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.266][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:53:31.266][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:53:31.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.268][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.269][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:53:31.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:53:31.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.279][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:53:31.280][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:53:31.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.282][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.283][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:53:31.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:53:31.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:53:31.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:53:31.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:53:31.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:53:31.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:31.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:31.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:53:31.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:53:31.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:31.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:31.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:31.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:31.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:31.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:31.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:31.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:31.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:31.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:31.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:31.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:31.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:53:31.320][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-09-09 13:53:31.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-09-09 13:53:31.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-09-09 13:53:31.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-09-09 13:53:31.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-09-09 13:53:31.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-09-09 13:53:31.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-09-09 13:53:31.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-09-09 13:53:31.340][biodb::testThat]
biodb.INFO [2025-09-09 13:53:31.342][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-09-09 13:53:31.343][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:53:31.343][biodb::testThat]
biodb.TRACE[2025-09-09 13:53:31.347][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:31.348][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:31.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.350][ef$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:53:31.351][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-09-09 13:53:31.378][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:31.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:31.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.382][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:31.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:31.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.386][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:31.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:31.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:53:31.392][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-09-09 13:53:31.397][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-09-09 13:53:31.426][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:53:31.442][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-09-09 13:53:31.444][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:53:31.446][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-09-09 13:53:31.470][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[2025-09-09 13:53:31.474][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:53:31.476][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:53:31.477][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-09 13:53:31.769][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-09-09 13:53:31.917][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:53:31.919][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-09-09 13:53:31.935][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-09-09 13:53:31.938][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-09-09 13:53:31.950][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:31.952][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:31.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.954][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:31.954][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:31.955][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:31.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:31.957][ef$get] fields variable is a list.
biodb.INFO [2025-09-09 13:53:31.962][biodb::testThat]
biodb.INFO [2025-09-09 13:53:31.963][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-09-09 13:53:31.964][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:53:31.965][biodb::testThat]
biodb.TRACE[2025-09-09 13:53:32.000][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:32.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:32.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.005][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:32.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:32.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.008][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:32.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:32.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:53:32.067][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:53:32.071][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:53:32.073][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-09-09 13:53:32.074][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:53:32.075][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-09-09 13:53:32.099][biodb::testThat]
biodb.INFO [2025-09-09 13:53:32.100][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-09-09 13:53:32.101][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:53:32.101][biodb::testThat]
biodb.TRACE[2025-09-09 13:53:32.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:53:32.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:53:32.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.127][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:53:32.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:53:32.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.131][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:53:32.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:53:32.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.134][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:53:32.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:53:32.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.137][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:32.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:32.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.140][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:32.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:32.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.144][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-09 13:53:32.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-09 13:53:32.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.147][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-09 13:53:32.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-09 13:53:32.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.150][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-09 13:53:32.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-09 13:53:32.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.154][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-09 13:53:32.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-09 13:53:32.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.176][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:53:32.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:53:32.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.180][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:53:32.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:53:32.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.184][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:53:32.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:53:32.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.187][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:53:32.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:53:32.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.197][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:32.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:32.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.201][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:32.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:32.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.204][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-09 13:53:32.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-09 13:53:32.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.207][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-09 13:53:32.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-09 13:53:32.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.211][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-09 13:53:32.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-09 13:53:32.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.214][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-09 13:53:32.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-09 13:53:32.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-09-09 13:53:32.225][biodb::testThat]
biodb.INFO [2025-09-09 13:53:32.226][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-09-09 13:53:32.227][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:53:32.227][biodb::testThat]
biodb.INFO [2025-09-09 13:53:32.236][biodb::testThat]
biodb.INFO [2025-09-09 13:53:32.237][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-09-09 13:53:32.238][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:53:32.239][biodb::testThat]
biodb.INFO [2025-09-09 13:53:32.247][biodb::testThat]
biodb.INFO [2025-09-09 13:53:32.248][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-09-09 13:53:32.249][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:53:32.250][biodb::testThat]
biodb.DEBUG[2025-09-09 13:53:32.254][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-09-09 13:53:32.428][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-09-09 13:53:32.649][biodb::testThat]
biodb.INFO [2025-09-09 13:53:32.650][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-09-09 13:53:32.651][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:53:32.652][biodb::testThat]
biodb.DEBUG[2025-09-09 13:53:32.745][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[2025-09-09 13:53:32.839][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:32.841][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:32.842][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.842][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.843][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:32.844][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:32.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.846][ef$get] fields variable is a list.
biodb.INFO [2025-09-09 13:53:32.848][biodb::testThat]
biodb.INFO [2025-09-09 13:53:32.849][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-09-09 13:53:32.850][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:53:32.851][biodb::testThat]
biodb.TRACE[2025-09-09 13:53:32.864][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:32.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:32.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.882][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:32.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:32.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:32.886][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:32.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:32.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:32.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:53:32.973][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:53:32.977][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:53:32.978][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-09-09 13:53:32.980][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:53:32.981][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-09-09 13:53:33.054][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:53:33.058][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:53:33.059][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-09-09 13:53:33.061][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:53:33.062][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-09-09 13:53:33.078][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-09 13:53:33.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-09 13:53:33.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.087][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:33.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:33.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.091][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:33.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:33.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:33.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:33.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.105][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:33.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:33.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:33.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:33.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:53:33.120][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:53:33.136][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:53:33.138][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:53:33.153][private$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[2025-09-09 13:53:33.231][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[2025-09-09 13:53:33.308][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:53:33.311][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-09-09 13:53:33.315][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-09-09 13:53:33.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:53:33.319][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:33.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:33.326][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:33.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:33.328][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:33.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:33.329][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-09-09 13:53:33.385][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:53:33.387][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-09-09 13:53:33.388][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:53:33.389][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:53:33.390][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:53:33.391][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:53:33.392][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:53:33.393][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:53:33.395][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:53:33.396][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:33.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:33.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:33.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:33.404][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:33.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:33.406][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-09-09 13:53:33.409][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:53:33.410][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:53:33.411][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-09-09 13:53:33.486][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-09-09 13:53:33.565][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:53:33.568][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-09-09 13:53:33.572][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-09-09 13:53:33.575][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-09-09 13:53:33.577][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:53:33.579][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:53:33.580][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:53:33.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:53:33.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:33.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:33.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:33.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:33.592][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:33.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:53:33.606][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:33.607][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:33.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.609][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:33.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:33.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.614][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:53:33.615][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:53:33.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.617][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.618][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:53:33.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:53:33.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.622][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:53:33.623][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:53:33.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.625][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.627][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:53:33.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:53:33.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.630][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:53:33.631][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:53:33.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.633][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.635][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:53:33.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:53:33.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.638][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:53:33.639][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:53:33.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.641][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.642][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:53:33.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:53:33.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.645][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:53:33.646][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:53:33.647][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.648][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.649][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:53:33.650][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:33.651][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.652][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.653][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:53:33.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:33.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.656][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:33.657][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:33.658][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.659][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:33.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:53:33.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.663][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:33.664][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:33.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.666][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.667][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:53:33.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:53:33.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.671][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:53:33.672][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:53:33.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.673][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.674][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:53:33.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:53:33.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.678][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:53:33.679][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:53:33.680][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.681][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.683][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:53:33.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:53:33.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:53:33.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:53:33.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:53:33.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:53:33.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:33.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:33.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:53:33.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:53:33.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:33.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:33.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:33.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:33.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:33.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:33.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:33.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:33.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:33.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:33.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:53:33.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:53:33.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:53:33.783][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-09-09 13:53:33.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:33.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:33.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:33.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:33.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:33.807][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:33.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:33.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:33.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:53:33.811][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[2025-09-09 13:53:33.815][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:53:33.816][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:53:33.818][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-09 13:53:33.903][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-09-09 13:53:33.975][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:53:33.977][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-09-09 13:53:33.982][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-09-09 13:53:34.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:53:34.001][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:34.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:34.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:34.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:34.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:34.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:53:34.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:34.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:34.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:34.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:34.015][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:34.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:34.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:34.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:53:34.018][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:34.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:53:34.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:53:34.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:53:34.022][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:53:34.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:34.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:34.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:34.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:34.032][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:34.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:34.033][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-09-09 13:53:34.034][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:53:34.036][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-09-09 13:53:34.037][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:53:34.038][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:53:34.039][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:53:34.040][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:53:34.041][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:53:34.042][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:53:34.067][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:53:34.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:53:34.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:53:34.075][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:53:34.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:53:34.077][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:53:34.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:53:34.079][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-09-09 13:53:34.083][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:53:34.084][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-09-09 13:53:34.085][rule$waitAsNeeded] Wait 0.0672851 second(s).
biodb.TRACE[2025-09-09 13:53:34.304][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-09-09 13:54:34.462][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892 does not exist.
biodb.TRACE[2025-09-09 13:54:34.463][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-09 13:54:34.464][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-09 13:54:34.465][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-09-09 13:54:34.808][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:34.811][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-09-09 13:54:34.815][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-09-09 13:54:34.818][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-09-09 13:54:34.820][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:34.821][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:34.823][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:34.824][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:34.825][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:34.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:34.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:34.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:34.834][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:34.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:34.838][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:34.839][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:34.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.841][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:34.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:34.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.845][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:34.846][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:34.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.848][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.849][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:34.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:34.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.853][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:34.854][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:34.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.855][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.857][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:34.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:34.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.861][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:34.861][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:34.862][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.863][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.864][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:34.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:34.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.868][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:34.869][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:34.870][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.870][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.872][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:34.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:34.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.926][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:34.927][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:34.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.929][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.931][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:34.931][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:34.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.933][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.934][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:34.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:34.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.938][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:34.939][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:34.940][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.940][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:34.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:34.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.945][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:34.946][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:34.947][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.948][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.949][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:34.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:34.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.953][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:34.954][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:34.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.955][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.956][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:34.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:34.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.960][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:34.961][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:34.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.962][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.963][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:34.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:34.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:34.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:34.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:34.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:34.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:34.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:34.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:34.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:34.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:34.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:34.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:34.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:34.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:34.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:34.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:34.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:34.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:34.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:34.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:34.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:34.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:34.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:34.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:35.000][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-09-09 13:54:35.001][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.015][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:35.039][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[2025-09-09 13:54:35.043][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:35.044][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-09-09 13:54:35.045][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:35.047][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-09-09 13:54:35.050][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:35.051][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:35.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:35.057][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:35.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:35.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:35.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:35.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.065][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.069][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:35.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:35.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:35.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:35.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:35.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:35.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:35.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:35.083][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-09-09 13:54:35.084][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:35.085][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-09-09 13:54:35.087][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:54:35.088][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:54:35.089][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:35.090][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:35.091][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:35.092][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:35.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:35.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:35.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:35.102][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:35.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:35.104][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:35.105][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.DEBUG[2025-09-09 13:54:35.106][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-09-09 13:54:35.109][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:35.110][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:35.111][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-09-09 13:54:35.189][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-09-09 13:54:35.261][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:35.264][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-09-09 13:54:35.277][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-09-09 13:54:35.280][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-09-09 13:54:35.282][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:35.283][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:35.284][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:35.286][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:35.287][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:35.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:35.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:35.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:35.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:35.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:35.299][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:35.300][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:35.301][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.302][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:35.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:35.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.307][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:35.308][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:35.309][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.310][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.311][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:35.312][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:35.313][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.314][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.315][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:35.316][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:35.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.318][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.319][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:35.320][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:35.321][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.321][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.322][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:35.323][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:35.324][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.325][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.326][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:35.327][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.329][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.330][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:35.331][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:35.332][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.332][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.333][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:35.334][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:35.335][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.336][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.337][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:35.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:35.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.341][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:35.342][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:35.343][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.344][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.345][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:35.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:35.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.349][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:35.350][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:35.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.351][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:35.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:35.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:35.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:35.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:35.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:35.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:35.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:35.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:35.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:35.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:35.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:35.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:35.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:35.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:35.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:35.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:35.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:35.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:35.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:35.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:35.399][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-09-09 13:54:35.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.404][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.408][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.411][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.414][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:35.419][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:35.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:35.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:35.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:35.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:35.427][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:35.428][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.DEBUG[2025-09-09 13:54:35.429][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-09-09 13:54:35.430][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:35.432][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-09-09 13:54:35.433][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:54:35.434][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:54:35.435][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:35.436][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:35.436][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:35.437][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:35.440][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:35.441][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:35.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:35.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:35.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:35.449][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:35.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:35.452][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-09-09 13:54:35.455][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:35.456][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:35.458][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-09-09 13:54:35.541][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-09-09 13:54:35.617][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:35.620][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-09-09 13:54:35.624][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-09-09 13:54:35.628][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-09-09 13:54:35.630][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:35.631][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:35.632][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:35.644][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:35.645][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:35.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:35.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:35.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:35.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:35.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:35.658][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:35.659][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:35.660][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.661][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:35.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:35.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.666][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:35.666][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:35.667][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.668][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.670][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:35.671][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:35.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.672][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.674][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:35.675][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:35.676][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.676][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.677][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:35.678][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:35.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.680][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.681][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:35.682][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:35.683][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.683][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.684][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:35.685][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.686][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.687][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.688][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:35.689][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:35.690][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.690][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.691][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:35.692][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:35.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.694][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.696][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:35.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:35.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.699][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:35.700][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:35.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.701][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.703][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:35.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:35.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.706][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:35.707][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:35.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.708][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.710][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:35.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:35.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:35.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:35.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:35.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:35.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:35.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:35.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:35.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:35.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:35.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:35.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:35.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:35.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:35.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:35.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:35.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:35.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:35.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:35.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:35.752][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-09-09 13:54:35.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.756][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.760][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:35.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:35.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:35.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:35.770][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:35.770][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:35.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:35.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:35.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:35.778][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:35.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:35.780][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-09-09 13:54:35.781][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:35.783][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-09-09 13:54:35.784][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:54:35.785][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:54:35.786][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:35.787][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:35.788][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:35.789][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:35.791][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:35.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:35.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:35.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:35.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:35.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:35.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:35.803][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-09-09 13:54:35.806][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:35.807][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:35.808][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-09-09 13:54:35.885][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-09-09 13:54:35.963][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:35.966][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-09-09 13:54:35.969][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-09-09 13:54:35.973][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-09-09 13:54:35.975][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:35.977][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:35.978][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:35.980][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:35.980][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:35.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:35.988][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:35.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:36.000][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:36.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:36.005][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.006][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.008][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.013][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:36.014][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:36.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.015][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.017][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:36.018][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:36.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.019][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.021][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:36.022][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:36.023][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.023][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.024][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:36.025][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:36.026][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.027][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.028][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:36.029][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:36.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.031][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.032][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:36.032][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.033][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.034][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.035][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:36.036][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:36.037][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.038][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.039][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:36.040][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:36.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.041][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.043][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:36.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:36.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.047][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:36.047][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:36.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.049][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.050][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:36.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:36.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.054][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:36.055][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:36.056][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.056][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:36.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:36.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:36.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:36.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:36.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:36.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:36.102][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-09-09 13:54:36.103][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.106][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.114][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:36.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:36.122][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:36.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:36.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:36.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:36.131][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:36.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:36.133][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-09-09 13:54:36.134][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:36.136][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-09-09 13:54:36.137][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:54:36.138][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:54:36.139][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:36.140][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:36.141][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:36.142][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:36.144][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:36.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:36.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:36.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:36.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:36.154][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:36.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:36.156][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-09-09 13:54:36.159][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:36.161][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:36.162][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-09-09 13:54:36.249][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-09-09 13:54:36.321][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:36.323][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-09-09 13:54:36.327][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-09-09 13:54:36.330][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-09-09 13:54:36.332][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:36.333][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:36.334][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:36.336][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:36.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:36.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:36.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:36.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:36.344][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:36.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:36.347][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.348][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.362][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.367][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:36.368][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:36.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.370][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.371][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:36.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:36.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.375][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:36.376][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:36.377][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.377][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.379][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:36.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:36.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.383][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:36.383][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:36.384][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.385][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.386][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:36.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:36.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.390][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:36.391][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:36.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.392][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.393][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:36.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:36.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.397][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:36.398][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:36.399][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.399][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.400][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:36.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:36.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.404][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:36.405][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.406][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.406][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.407][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:36.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.411][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:36.412][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:36.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.413][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:36.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:36.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.418][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:36.419][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:36.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.420][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.422][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:36.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:36.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.425][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:36.426][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:36.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.428][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.429][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:36.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:36.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.432][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:36.433][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:36.434][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.435][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.436][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:36.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:36.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:36.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:36.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.443][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:36.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:36.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.458][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:36.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:36.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:36.483][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-09-09 13:54:36.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.487][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.490][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:36.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:36.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:36.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:36.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:36.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:36.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:36.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:36.506][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-09-09 13:54:36.507][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:36.508][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-09-09 13:54:36.509][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:54:36.510][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:54:36.511][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:36.512][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:36.513][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:36.514][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:36.516][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:36.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:36.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:36.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:36.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:36.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:36.526][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[2025-09-09 13:54:36.527][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-09-09 13:54:36.530][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:36.531][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:36.532][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-09-09 13:54:36.615][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-09-09 13:54:36.693][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:36.695][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-09-09 13:54:36.699][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-09-09 13:54:36.711][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-09-09 13:54:36.713][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:36.714][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:36.715][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:36.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:36.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:36.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:36.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:36.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:36.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:36.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:36.730][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.731][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.732][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.732][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.737][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:36.738][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:36.739][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.740][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.741][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:36.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:36.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.744][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:36.745][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:36.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.747][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.748][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:36.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:36.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.751][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:36.752][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:36.753][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.754][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.755][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:36.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:36.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.758][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:36.759][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:36.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.761][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.762][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:36.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:36.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.765][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:36.766][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:36.767][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.768][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.769][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:36.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:36.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.772][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:36.773][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.774][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.776][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:36.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.779][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:36.780][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:36.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.781][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:36.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:36.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.786][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:36.787][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:36.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.788][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.790][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:36.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:36.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.793][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:36.794][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:36.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.803][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.804][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:36.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:36.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.808][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:36.809][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:36.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.811][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.812][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:36.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:36.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:36.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:36.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:36.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:36.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:36.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:36.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:36.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:36.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:36.854][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-09-09 13:54:36.856][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.860][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:36.864][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:36.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:36.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:36.869][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:36.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:36.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:36.877][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:36.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:36.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:36.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:36.880][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-09-09 13:54:36.881][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:36.883][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-09-09 13:54:36.884][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:54:36.885][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:54:36.886][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:36.887][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:36.889][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:36.890][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:36.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:36.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:36.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:36.911][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:36.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:36.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:36.915][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[2025-09-09 13:54:36.916][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-09-09 13:54:36.919][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:36.920][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:36.922][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-09-09 13:54:37.006][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-09-09 13:54:37.081][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:37.083][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-09-09 13:54:37.087][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-09-09 13:54:37.090][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-09-09 13:54:37.091][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:37.093][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:37.094][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:37.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:37.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:37.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:37.102][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:37.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:37.104][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:37.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:37.108][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.109][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.110][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.111][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.116][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:37.116][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:37.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.118][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.119][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:37.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:37.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.123][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:37.124][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:37.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.125][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.126][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:37.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:37.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.130][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:37.131][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:37.131][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.132][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.133][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:37.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:37.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.137][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:37.138][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:37.139][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.140][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.141][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:37.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:37.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.144][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:37.145][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:37.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.147][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.148][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:37.149][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.150][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.152][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:37.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.155][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:37.156][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:37.157][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.158][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:37.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:37.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.174][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:37.175][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:37.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.176][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.177][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:37.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:37.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.181][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:37.182][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:37.183][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.183][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.184][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:37.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:37.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.188][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:37.189][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:37.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.191][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.192][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:37.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:37.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:37.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:37.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:37.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:37.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.205][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:37.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:37.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:37.232][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-09-09 13:54:37.233][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.237][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.240][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:37.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:37.245][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:37.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:37.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:37.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:37.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:37.254][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.DEBUG[2025-09-09 13:54:37.256][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-09-09 13:54:37.263][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:37.266][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-09-09 13:54:37.268][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:54:37.269][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:54:37.270][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:37.271][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:37.272][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:37.273][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:37.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:37.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:37.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:37.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:37.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:37.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:37.287][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[2025-09-09 13:54:37.288][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-09-09 13:54:37.291][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:37.292][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:37.294][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-09-09 13:54:37.375][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-09-09 13:54:37.452][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:37.455][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-09-09 13:54:37.458][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-09-09 13:54:37.461][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-09-09 13:54:37.462][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:37.464][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:37.465][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:37.466][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:37.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:37.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:37.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:37.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:37.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:37.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:37.478][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.479][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.480][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.481][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.485][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:37.486][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:37.487][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.488][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.489][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:37.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:37.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.492][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:37.493][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:37.494][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.495][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.496][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:37.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:37.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.499][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:37.500][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:37.501][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.501][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.502][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:37.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:37.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.506][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:37.507][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:37.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.508][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.509][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:37.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:37.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.519][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:37.523][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:37.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.525][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.527][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:37.527][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.529][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.530][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:37.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.533][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:37.534][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:37.535][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.536][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:37.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:37.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.540][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:37.541][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:37.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.543][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.544][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:37.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:37.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.547][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:37.548][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:37.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.550][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.551][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:37.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:37.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.554][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:37.555][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:37.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.556][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.557][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:37.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:37.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.561][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:37.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:37.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:37.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:37.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:37.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:37.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:37.593][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-09-09 13:54:37.594][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.597][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.608][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:37.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:37.612][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:37.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:37.618][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:37.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:37.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:37.621][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[2025-09-09 13:54:37.622][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-09-09 13:54:37.623][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:37.624][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-09-09 13:54:37.626][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:54:37.627][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:54:37.629][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:37.630][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:37.631][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:37.632][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:37.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:37.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:37.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:37.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:37.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:37.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:37.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:37.646][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-09-09 13:54:37.650][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:37.651][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:37.652][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-09-09 13:54:37.727][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-09-09 13:54:37.807][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:37.810][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-09-09 13:54:37.814][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-09-09 13:54:37.817][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-09-09 13:54:37.819][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:37.821][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:37.822][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:37.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:37.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:37.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:37.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:37.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:37.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:37.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:37.837][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.838][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.839][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.841][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.846][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:37.846][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:37.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.848][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.849][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:37.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:37.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.853][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:37.854][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:37.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.855][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.856][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:37.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:37.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.869][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:37.871][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:37.872][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.873][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.874][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:37.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:37.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.877][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:37.878][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:37.879][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.880][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.881][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:37.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:37.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.884][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:37.885][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:37.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.887][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.888][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:37.889][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.890][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.890][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.891][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:37.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.895][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:37.896][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:37.896][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.897][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:37.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:37.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.902][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:37.902][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:37.903][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.904][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.905][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:37.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:37.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.908][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:37.909][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:37.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.911][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.912][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:37.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:37.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.915][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:37.916][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:37.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.917][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.918][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:37.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:37.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.922][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:37.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:37.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.926][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:37.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:37.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.933][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:37.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:37.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:37.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:37.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:37.967][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-09-09 13:54:37.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.971][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:37.975][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:37.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:37.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:37.978][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:37.979][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:37.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:37.985][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:37.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:37.987][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:37.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:37.989][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-09-09 13:54:37.990][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:37.992][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-09-09 13:54:37.993][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:54:37.994][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:54:37.995][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:37.996][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:37.997][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:37.997][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:38.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:38.001][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:38.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:38.007][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:38.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:38.009][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:38.010][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.DEBUG[2025-09-09 13:54:38.011][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-09-09 13:54:38.014][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:38.015][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:38.016][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-09-09 13:54:38.095][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-09-09 13:54:38.173][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:38.175][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-09-09 13:54:38.179][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-09-09 13:54:38.181][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-09-09 13:54:38.183][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:38.184][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:38.185][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:38.187][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:38.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:38.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:38.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:38.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:38.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:38.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:38.200][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:38.202][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:38.202][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.203][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:38.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:38.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.219][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:38.221][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:38.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.223][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.225][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:38.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:38.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.229][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:38.230][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:38.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.231][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.233][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:38.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:38.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.236][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:38.237][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:38.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.239][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.240][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:38.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:38.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.244][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:38.245][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:38.246][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.247][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.248][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:38.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:38.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.252][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:38.253][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:38.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.254][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.255][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:38.256][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:38.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.258][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.259][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:38.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:38.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.263][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:38.264][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:38.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.265][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:38.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:38.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.270][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:38.270][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:38.271][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.272][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.273][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:38.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:38.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.277][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:38.278][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:38.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.279][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.280][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:38.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:38.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.284][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:38.284][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:38.285][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.286][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.287][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:38.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:38.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.291][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:38.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:38.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:38.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:38.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:38.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:38.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:38.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:38.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:38.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:38.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:38.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:38.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:38.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:38.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:38.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:38.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:38.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:38.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:38.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:38.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:38.334][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-09-09 13:54:38.335][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:38.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:38.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:38.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:38.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:38.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:38.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:38.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:38.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:38.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:38.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:38.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:38.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:38.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:38.357][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-09-09 13:54:38.358][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:38.360][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-09-09 13:54:38.361][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:54:38.363][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:54:38.364][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:38.365][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:38.366][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:38.367][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:38.370][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:38.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:38.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:38.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:38.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:38.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:38.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:38.381][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-09-09 13:54:38.385][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:38.386][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:38.387][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-09-09 13:54:38.463][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-09-09 13:54:38.540][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:38.542][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-09-09 13:54:38.546][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-09-09 13:54:38.550][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-09-09 13:54:38.552][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:38.553][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:38.554][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:38.556][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:38.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:38.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:38.579][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:38.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:38.581][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:38.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:38.584][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:38.585][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:38.586][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.587][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:38.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:38.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.592][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:38.593][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:38.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.594][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.595][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:38.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:38.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.599][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:38.600][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:38.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.601][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.603][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:38.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:38.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.606][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:38.607][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:38.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.609][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.610][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:38.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:38.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.613][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:38.614][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:38.615][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.616][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.617][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:38.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:38.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.620][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:38.621][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:38.622][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.623][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.624][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:38.625][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:38.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.627][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.628][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:38.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:38.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.631][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:38.632][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:38.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.634][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:38.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:38.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.639][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:38.640][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:38.641][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.642][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.643][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:38.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:38.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.648][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:38.649][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:38.649][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.650][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.651][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:38.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:38.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.655][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:38.656][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:38.657][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.658][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.659][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:38.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:38.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.670][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:38.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:38.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:38.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:38.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:38.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:38.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:38.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:38.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:38.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:38.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:38.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:38.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:38.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:38.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:38.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:38.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:38.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:38.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:38.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:38.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:38.706][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-09-09 13:54:38.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:38.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:38.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:38.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:38.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.714][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:38.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:38.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:38.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:38.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:38.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:38.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:38.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:38.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:38.727][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[2025-09-09 13:54:38.728][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-09-09 13:54:38.729][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:38.731][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-09-09 13:54:38.732][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:54:38.733][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:54:38.734][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:38.735][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:38.736][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:38.737][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:38.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:38.740][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:38.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:38.747][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:38.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:38.748][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:38.749][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[2025-09-09 13:54:38.750][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-09-09 13:54:38.753][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:38.754][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:38.756][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-09-09 13:54:38.838][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-09-09 13:54:38.914][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:38.917][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-09-09 13:54:38.921][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-09-09 13:54:38.924][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-09-09 13:54:38.925][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:38.927][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:38.928][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:38.929][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:38.930][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:38.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:38.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:38.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:38.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:38.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:38.942][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:38.943][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:38.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.945][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:38.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:38.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.950][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:38.951][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:38.952][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.952][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.954][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:38.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:38.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.957][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:38.958][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:38.959][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.959][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.960][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:38.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:38.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.964][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:38.965][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:38.965][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.966][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.967][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:38.968][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:38.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.970][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.971][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:38.972][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:38.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.974][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.975][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:38.976][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:38.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.977][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.978][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:38.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:38.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.982][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:38.983][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:38.984][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.984][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:38.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:38.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.989][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:38.990][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:38.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.991][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.993][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:38.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:38.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.996][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:38.997][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:38.998][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:38.998][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:38.999][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:39.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:39.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.012][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:39.013][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:39.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.016][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.017][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:39.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:39.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:39.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:39.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:39.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:39.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:39.052][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-09-09 13:54:39.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:39.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:39.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:39.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:39.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:39.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:39.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:39.062][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:39.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:39.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:39.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:39.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:39.071][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:39.072][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[2025-09-09 13:54:39.073][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-09-09 13:54:39.074][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:39.076][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-09-09 13:54:39.077][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:54:39.078][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:54:39.079][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:39.080][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:39.081][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:39.082][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:39.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:39.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:39.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:39.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:39.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:39.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:39.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:39.096][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-09-09 13:54:39.099][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:39.106][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:39.108][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-09-09 13:54:39.182][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-09-09 13:54:39.256][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:39.259][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-09-09 13:54:39.263][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-09-09 13:54:39.265][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-09-09 13:54:39.268][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:39.269][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:39.270][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:39.272][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:39.273][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:39.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:39.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:39.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:39.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:39.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:39.285][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.286][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.288][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.293][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:39.294][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:39.295][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.295][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.297][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:39.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:39.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.300][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:39.301][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:39.302][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.303][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.304][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:39.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:39.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.307][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:39.308][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:39.309][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.309][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.311][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:39.311][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:39.312][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.313][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.314][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:39.315][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:39.316][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.316][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.317][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:39.318][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:39.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.320][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.321][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:39.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:39.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.324][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:39.325][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:39.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.327][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:39.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:39.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.331][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:39.332][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:39.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.334][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.335][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:39.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:39.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.339][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:39.340][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:39.340][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.341][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.352][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:39.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:39.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.358][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:39.359][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:39.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.360][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:39.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:39.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.365][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:39.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:39.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:39.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:39.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:39.399][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-09-09 13:54:39.400][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:39.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:39.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.403][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:39.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:39.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.407][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:39.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:39.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:39.410][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:39.411][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:39.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:39.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:39.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:39.419][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:39.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:39.421][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-09-09 13:54:39.422][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:39.424][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-09-09 13:54:39.425][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:54:39.427][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:54:39.428][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:39.428][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:39.429][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:39.430][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:39.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:39.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:39.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:39.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:39.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:39.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:39.443][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[2025-09-09 13:54:39.451][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-09-09 13:54:39.455][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:39.456][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:39.458][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-09-09 13:54:39.540][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-09-09 13:54:39.611][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:39.614][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-09-09 13:54:39.617][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-09-09 13:54:39.620][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-09-09 13:54:39.622][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:39.623][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:39.624][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:39.626][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:39.627][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:39.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:39.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:39.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:39.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:39.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:39.639][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.640][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.641][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.642][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.646][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:39.647][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:39.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.649][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.650][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:39.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:39.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.653][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:39.654][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:39.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.656][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.657][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:39.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:39.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.660][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:39.661][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:39.662][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.663][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.664][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:39.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:39.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.668][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:39.669][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:39.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.670][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.671][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:39.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:39.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.675][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:39.676][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:39.677][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.677][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.678][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:39.679][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:39.680][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.681][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.682][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:39.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:39.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.686][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:39.687][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:39.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.688][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:39.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:39.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.693][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:39.707][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:39.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.709][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.711][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:39.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:39.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.717][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:39.718][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:39.719][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.720][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.722][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:39.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:39.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.728][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:39.729][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:39.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.731][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.733][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:39.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:39.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:39.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:39.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.745][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:39.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:39.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:39.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:39.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:39.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:39.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:39.790][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-09-09 13:54:39.791][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:39.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:39.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:39.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:39.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:39.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:39.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:39.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:39.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:39.801][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:39.802][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:39.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:39.809][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:39.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:39.811][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:39.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:39.813][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-09-09 13:54:39.814][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:39.815][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-09-09 13:54:39.816][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:54:39.818][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:54:39.826][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:39.828][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:39.829][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:39.830][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:39.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:39.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:39.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:39.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:39.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:39.844][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:39.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:39.846][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-09-09 13:54:39.849][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:39.850][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:39.851][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-09-09 13:54:39.929][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-09-09 13:54:40.008][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:40.010][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-09-09 13:54:40.014][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-09-09 13:54:40.017][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-09-09 13:54:40.019][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:40.020][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:40.021][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:40.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:40.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:40.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:40.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:40.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:40.032][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:40.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:40.035][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.036][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.037][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.038][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.042][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:40.043][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:40.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.045][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.046][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:40.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:40.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.049][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:40.050][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:40.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.052][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.053][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:40.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:40.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.057][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:40.058][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:40.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.060][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.061][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:40.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:40.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.065][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:40.066][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:40.067][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.068][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.069][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:40.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:40.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.075][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:40.081][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:40.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.086][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.099][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:40.101][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.103][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.105][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:40.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.110][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:40.111][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:40.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.112][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:40.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:40.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.118][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:40.119][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:40.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.121][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.122][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:40.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:40.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.126][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:40.127][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:40.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.129][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.130][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:40.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:40.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.135][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:40.136][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:40.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.138][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.139][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:40.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:40.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:40.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:40.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:40.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:40.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:40.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:40.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:40.177][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-09-09 13:54:40.178][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.182][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:40.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:40.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:40.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:40.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:40.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:40.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:40.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:40.209][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-09-09 13:54:40.210][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:40.212][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-09-09 13:54:40.213][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:54:40.215][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:54:40.216][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:40.217][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:40.218][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:40.219][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:40.221][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:40.223][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:40.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:40.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:40.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:40.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:40.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:40.234][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-09-09 13:54:40.237][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:40.239][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:40.241][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-09-09 13:54:40.321][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-09-09 13:54:40.397][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:40.399][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-09-09 13:54:40.403][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-09-09 13:54:40.406][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-09-09 13:54:40.407][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:40.409][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:40.410][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:40.411][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:40.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:40.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:40.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:40.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:40.422][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:40.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:40.426][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.427][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.428][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.434][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:40.435][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:40.436][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.437][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.438][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:40.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:40.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.441][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:40.442][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:40.443][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.444][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.445][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:40.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:40.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.449][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:40.449][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:40.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.458][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.463][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:40.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:40.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.468][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:40.469][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:40.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.471][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.473][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:40.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:40.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.476][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:40.477][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:40.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.479][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.480][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:40.481][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.483][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.484][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:40.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.488][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:40.489][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:40.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.490][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:40.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:40.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.496][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:40.497][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:40.498][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.498][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.500][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:40.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:40.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.505][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:40.506][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:40.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.507][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.509][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:40.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:40.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.513][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:40.514][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:40.515][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.517][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.518][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:40.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:40.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:40.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:40.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:40.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:40.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:40.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:40.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:40.566][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-09-09 13:54:40.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:40.577][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:40.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:40.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:40.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:40.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:40.588][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:40.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:40.590][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-09-09 13:54:40.591][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:40.593][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-09-09 13:54:40.594][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:54:40.595][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:54:40.596][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:40.597][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:40.598][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:40.599][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:40.601][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:40.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:40.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:40.609][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:40.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:40.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:40.612][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[2025-09-09 13:54:40.614][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-09-09 13:54:40.617][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:40.618][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:40.619][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-09-09 13:54:40.700][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-09-09 13:54:40.778][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:40.780][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-09-09 13:54:40.784][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-09-09 13:54:40.786][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-09-09 13:54:40.788][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:40.789][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:40.790][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:40.792][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:40.793][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:40.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:40.800][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:40.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:40.802][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:40.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:40.805][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.806][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.809][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.814][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:40.815][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:40.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.828][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.830][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:40.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:40.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.834][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:40.835][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:40.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.837][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.839][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:40.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:40.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.842][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:40.843][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:40.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.845][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.846][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:40.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:40.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.850][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:40.851][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:40.851][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.853][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.854][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:40.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:40.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.858][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:40.859][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:40.860][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.860][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.862][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:40.863][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.864][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.865][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:40.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.869][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:40.870][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:40.870][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.871][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:40.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:40.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.876][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:40.877][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:40.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.878][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.879][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:40.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:40.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.883][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:40.884][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:40.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.885][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.886][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:40.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:40.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.891][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:40.892][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:40.893][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.894][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.895][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:40.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:40.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:40.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:40.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.902][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:40.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:40.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:40.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:40.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:40.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:40.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:40.943][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-09-09 13:54:40.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:40.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:40.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:40.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:40.954][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:40.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:40.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:40.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:40.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:40.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:40.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:40.965][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-09-09 13:54:40.966][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:40.968][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-09-09 13:54:40.969][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:54:40.970][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:54:40.971][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:40.972][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:40.973][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:40.974][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:40.977][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:40.977][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:40.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:40.985][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:40.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:40.986][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:40.987][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[2025-09-09 13:54:40.988][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-09-09 13:54:40.991][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:40.992][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:40.993][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-09-09 13:54:41.070][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-09-09 13:54:41.142][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:41.144][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-09-09 13:54:41.149][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-09-09 13:54:41.152][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-09-09 13:54:41.154][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:41.155][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:41.156][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:41.158][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:41.159][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:41.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:41.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:41.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:41.180][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:41.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:41.183][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:41.184][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:41.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.186][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:41.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:41.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.191][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:41.192][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:41.193][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.193][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.195][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:41.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:41.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.199][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:41.200][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:41.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.202][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.204][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:41.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:41.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.208][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:41.209][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:41.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.211][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.212][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:41.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:41.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.215][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:41.216][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:41.217][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.218][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.219][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:41.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:41.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.222][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:41.223][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:41.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.225][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.226][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:41.227][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:41.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.229][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.230][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:41.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:41.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.233][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:41.235][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:41.236][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.237][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:41.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:41.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.242][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:41.243][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:41.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.244][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.246][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:41.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:41.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.250][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:41.251][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:41.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.253][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.254][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:41.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:41.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.258][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:41.259][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:41.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.261][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.262][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:41.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:41.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:41.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:41.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:41.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:41.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:41.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:41.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:41.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:41.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:41.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:41.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:41.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:41.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:41.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:41.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:41.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:41.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:41.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:41.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:41.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:41.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:41.311][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-09-09 13:54:41.312][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:41.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:41.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:41.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:41.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.320][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:41.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:41.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:41.324][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:41.325][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:41.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:41.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:41.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:41.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:41.335][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[2025-09-09 13:54:41.336][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-09-09 13:54:41.337][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:41.338][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-09-09 13:54:41.340][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:54:41.341][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:54:41.342][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:41.343][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:41.344][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:41.344][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:41.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:41.348][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:41.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:41.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:41.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:41.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:41.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:41.359][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-09-09 13:54:41.362][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:41.369][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:41.372][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-09-09 13:54:41.452][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-09-09 13:54:41.525][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:41.528][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-09-09 13:54:41.532][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-09-09 13:54:41.535][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-09-09 13:54:41.536][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:41.537][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:41.539][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:41.540][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:41.541][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:41.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:41.548][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:41.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:41.551][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:41.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:41.555][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:41.556][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:41.557][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.558][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:41.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:41.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.563][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:41.564][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:41.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.566][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.567][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:41.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:41.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.571][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:41.572][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:41.572][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.573][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.575][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:41.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:41.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.578][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:41.579][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:41.580][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.581][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.582][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:41.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:41.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.585][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:41.586][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:41.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.588][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:41.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:41.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.593][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:41.594][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:41.595][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.596][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.597][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:41.598][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:41.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.600][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.601][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:41.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:41.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.605][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:41.606][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:41.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.608][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:41.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:41.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.613][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:41.614][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:41.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.628][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.630][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:41.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:41.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.635][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:41.636][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:41.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.637][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.638][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:41.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:41.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.642][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:41.643][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:41.644][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.645][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.646][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:41.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:41.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:41.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:41.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.654][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:41.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:41.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:41.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:41.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:41.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:41.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:41.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:41.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:41.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:41.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:41.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:41.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:41.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:41.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:41.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:41.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:41.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:41.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:41.685][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-09-09 13:54:41.686][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:41.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:41.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.689][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:41.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:41.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.693][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:41.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:41.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:41.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:41.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:41.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:41.703][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:41.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:41.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:41.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:41.707][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-09-09 13:54:41.708][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:41.710][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-09-09 13:54:41.711][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:54:41.712][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:54:41.720][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:41.721][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:41.723][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:41.724][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:41.727][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:41.728][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:41.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:41.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:41.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:41.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:41.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:41.738][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-09-09 13:54:41.741][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:41.742][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:41.743][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-09-09 13:54:41.827][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-09-09 13:54:41.906][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:41.909][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-09-09 13:54:41.913][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-09-09 13:54:41.915][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-09-09 13:54:41.917][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:41.918][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:41.919][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:41.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:41.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:41.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:41.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:41.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:41.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:41.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:41.933][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:41.934][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:41.935][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.936][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:41.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:41.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.941][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:41.942][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:41.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.943][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.944][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:41.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:41.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.948][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:41.949][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:41.950][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.950][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.952][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:41.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:41.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.955][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:41.956][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:41.957][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.958][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.959][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:41.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:41.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.962][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:41.963][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:41.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.965][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.966][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:41.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:41.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.970][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:41.970][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:41.971][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.983][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.985][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:41.986][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:41.987][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.988][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.990][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:41.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:41.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.993][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:41.994][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:41.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.996][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:41.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:41.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:41.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:41.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.000][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:42.001][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:42.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.003][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.004][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:42.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:42.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.008][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:42.009][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:42.010][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.010][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.012][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:42.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:42.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.015][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:42.016][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:42.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.018][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.019][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:42.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:42.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:42.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:42.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.027][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:42.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:42.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:42.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:42.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:42.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:42.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:42.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:42.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:42.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:42.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:42.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:42.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:42.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:42.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:42.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:42.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:42.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:42.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:42.058][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-09-09 13:54:42.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:42.312][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[2025-09-09 13:54:42.316][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:42.317][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-09-09 13:54:42.318][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:42.320][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-09-09 13:54:42.323][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:42.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:42.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:42.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:42.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:42.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:42.333][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.TRACE[2025-09-09 13:54:42.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.337][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:42.344][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:42.345][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:42.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:42.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:42.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:42.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:42.354][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.TRACE[2025-09-09 13:54:42.355][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.370][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:42.374][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:42.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:42.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:42.381][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:42.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:42.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:42.384][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.TRACE[2025-09-09 13:54:42.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:42.403][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:42.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:42.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:42.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:42.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:42.412][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:42.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:42.414][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.418][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.426][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.431][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:42.435][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:42.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:42.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:42.444][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:42.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:42.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:42.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:42.449][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.453][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:42.460][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:42.461][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:42.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:42.468][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:42.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:42.471][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:42.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:42.473][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.481][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:42.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:42.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:42.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:42.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:42.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:42.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:42.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:42.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.500][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.504][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:42.507][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:42.508][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:42.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:42.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:42.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:42.516][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:42.517][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.TRACE[2025-09-09 13:54:42.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.526][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:42.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:42.530][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:42.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:42.537][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:42.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:42.539][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:42.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:42.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.546][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:42.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:42.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:42.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:42.561][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:42.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:42.563][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:42.564][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[2025-09-09 13:54:42.565][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:42.576][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:42.577][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:42.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:42.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:42.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:42.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:42.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:42.588][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.591][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:42.599][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:42.600][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:42.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:42.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:42.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:42.608][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:42.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:42.610][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:42.622][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:42.623][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:42.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:42.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:42.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:42.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:42.634][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.TRACE[2025-09-09 13:54:42.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.639][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.643][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:42.647][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:42.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:42.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:42.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:42.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:42.657][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:42.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:42.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.673][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:42.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:42.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:42.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:42.683][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:42.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:42.685][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:42.686][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.TRACE[2025-09-09 13:54:42.687][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.694][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:42.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:42.698][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:42.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:42.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:42.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:42.706][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:42.707][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[2025-09-09 13:54:42.708][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.712][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.717][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:42.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:42.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:42.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:42.727][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:42.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:42.729][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:42.729][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.TRACE[2025-09-09 13:54:42.731][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:42.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:42.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:42.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:42.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:42.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:42.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:42.751][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[2025-09-09 13:54:42.752][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.756][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.760][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:42.763][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:42.764][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:42.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:42.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:42.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:42.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:42.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:42.775][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.778][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:42.786][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:42.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:42.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:42.794][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:42.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:42.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:42.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:42.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.806][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:42.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:42.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:42.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:42.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:42.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:42.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:42.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:42.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:42.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:42.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:42.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:42.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:42.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:42.868][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[2025-09-09 13:54:42.871][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:42.872][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:42.874][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-09 13:54:42.947][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-09-09 13:54:43.022][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:43.025][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-09-09 13:54:43.030][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-09-09 13:54:43.034][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:43.037][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:43.038][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:43.040][private$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[2025-09-09 13:54:43.113][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[2025-09-09 13:54:43.191][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:43.193][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-09-09 13:54:43.198][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-09-09 13:54:43.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:43.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:43.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:43.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:43.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:43.211][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:43.212][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[2025-09-09 13:54:43.213][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-09-09 13:54:43.214][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:43.215][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-09-09 13:54:43.217][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:54:43.218][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:54:43.219][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:43.220][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:43.221][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:43.222][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:43.225][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:43.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:43.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:43.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:43.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:43.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:43.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:43.237][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-09-09 13:54:43.240][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:43.241][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:43.242][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-09-09 13:54:43.341][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-09-09 13:54:43.425][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:43.427][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-09-09 13:54:43.432][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-09-09 13:54:43.436][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-09-09 13:54:43.438][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:43.439][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:43.441][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:43.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:43.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:43.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:43.452][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:43.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:43.454][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:43.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:43.459][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:43.461][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:43.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.463][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:43.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:43.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.467][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:43.468][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:43.469][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.470][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.471][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:43.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:43.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.476][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:43.477][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:43.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.479][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.481][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:43.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:43.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.486][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:43.487][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:43.489][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.490][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.491][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:43.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:43.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.495][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:43.495][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:43.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.497][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.498][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:43.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:43.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.502][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:43.519][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:43.520][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.521][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.522][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:43.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:43.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.526][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:43.528][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:43.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.529][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.531][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:43.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:43.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.534][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:43.535][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:43.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.537][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:43.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:43.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.541][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:43.542][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:43.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.544][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.545][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:43.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:43.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.548][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:43.549][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:43.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.551][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.552][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:43.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:43.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.555][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:43.557][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:43.558][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.559][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.560][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:43.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:43.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:43.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:43.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:43.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:43.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:43.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:43.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:43.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:43.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:43.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:43.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:43.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:43.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:43.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:43.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:43.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:43.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:43.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:43.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:43.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:43.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:43.598][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-09-09 13:54:43.599][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:43.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:43.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:43.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:43.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:43.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:43.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:43.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:43.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:43.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:43.621][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:43.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:43.623][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:43.624][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.TRACE[2025-09-09 13:54:43.625][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:43.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:43.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:43.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:43.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:43.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:43.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:43.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:43.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:43.637][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:43.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:43.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:43.644][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:43.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:43.646][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:43.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:43.647][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-09-09 13:54:43.649][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:43.650][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-09-09 13:54:43.652][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:54:43.653][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:54:43.654][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:43.655][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:43.655][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:43.656][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:43.659][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:43.660][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:43.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:43.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:43.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:43.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:43.668][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[2025-09-09 13:54:43.670][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-09-09 13:54:43.673][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:43.674][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-09-09 13:54:43.676][rule$waitAsNeeded] Wait 0.198272 second(s).
biodb.TRACE[2025-09-09 13:54:44.026][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-09-09 13:54:44.102][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-09-09 13:54:44.182][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:44.185][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-09-09 13:54:44.190][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-09-09 13:54:44.193][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-09-09 13:54:44.195][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:44.196][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:44.197][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:44.199][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.212][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:44.213][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:44.213][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.214][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:44.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:44.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.219][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:44.220][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:44.221][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.222][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.223][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:44.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:44.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.226][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:44.227][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:44.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.229][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.230][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:44.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:44.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.233][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:44.234][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:44.235][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.236][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.237][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:44.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:44.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.240][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:44.241][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:44.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.243][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.244][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:44.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:44.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.247][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:44.248][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:44.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.249][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.251][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:44.251][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:44.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.253][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.254][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:44.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:44.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.258][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.259][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.259][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.260][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.265][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:44.265][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:44.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.267][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.268][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:44.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:44.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.272][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:44.273][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:44.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.275][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.276][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:44.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:44.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.280][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:44.280][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:44.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.282][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.283][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:44.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:44.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:44.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:44.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:44.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:44.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:44.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:44.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:44.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:44.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:44.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:44.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:44.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:44.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:44.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:44.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:44.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:44.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:44.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:44.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:44.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:44.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.320][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-09-09 13:54:44.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.325][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.351][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:44.355][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:44.356][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-09-09 13:54:44.357][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:44.369][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-09-09 13:54:44.372][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.373][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.387][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.390][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.394][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.411][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.418][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.422][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.429][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.431][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.433][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.440][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.451][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.458][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.475][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.479][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.480][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.488][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.490][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.493][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.500][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.501][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.508][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.515][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.522][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.523][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.531][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.533][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.545][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.552][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.554][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.590][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.591][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.601][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.607][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.616][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.628][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.640][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.641][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.647][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.649][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.651][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.654][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.658][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.671][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.680][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.684][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.701][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.713][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.732][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.733][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.750][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.762][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.783][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.804][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.822][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.824][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.834][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.857][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:44.861][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:44.863][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-09-09 13:54:44.864][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:44.865][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-09-09 13:54:44.869][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.869][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.891][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.900][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.904][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.918][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.926][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.928][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.931][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.951][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.953][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.955][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.958][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.965][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.968][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.972][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:44.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:44.980][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:44.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:44.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.986][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:44.989][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:44.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:44.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:44.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:44.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:44.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:44.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.001][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:45.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.006][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.009][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:45.013][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:45.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:45.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:45.020][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:45.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:45.033][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:45.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:45.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:45.040][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.042][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:45.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.050][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:45.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:45.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:45.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:45.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:45.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:45.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:45.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:45.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:45.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:45.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:45.102][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:45.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:45.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:45.108][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.110][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:45.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.115][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:45.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:45.122][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:45.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:45.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:45.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.135][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.138][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:45.141][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:45.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:45.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:45.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.150][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:45.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:45.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:45.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:45.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:45.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.171][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:45.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:45.183][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:45.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:45.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:45.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:45.193][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.197][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:45.203][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:45.204][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:45.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:45.210][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:45.214][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:45.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:45.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:45.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:45.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:45.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.240][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:45.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:45.244][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:45.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:45.250][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.252][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:45.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.257][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:45.264][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:45.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:45.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:45.272][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:45.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:45.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:45.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:45.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:45.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:45.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.324][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-09-09 13:54:45.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-09-09 13:54:45.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-09-09 13:54:45.337][biodb::testThat]
biodb.INFO [2025-09-09 13:54:45.338][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-09-09 13:54:45.339][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:54:45.340][biodb::testThat]
biodb.TRACE[2025-09-09 13:54:45.343][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-09 13:54:45.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-09 13:54:45.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.350][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.353][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.357][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:45.364][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:45.365][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:45.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:45.371][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.373][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:45.376][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:45.380][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:45.381][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-09-09 13:54:45.383][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:45.384][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-09-09 13:54:45.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:45.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:45.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:45.394][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:45.398][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.413][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:45.417][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:45.421][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:45.422][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-09-09 13:54:45.424][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:45.425][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-09-09 13:54:45.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:45.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:45.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:45.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:45.439][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.446][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:45.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:45.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:45.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:45.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:45.460][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.463][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:45.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:45.470][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-09-09 13:54:45.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:45.473][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:45.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:45.479][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:45.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.490][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:45.491][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-09-09 13:54:45.492][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-09-09 13:54:45.493][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-09-09 13:54:45.493][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:45.494][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.495][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.497][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.498][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.499][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.499][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.500][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.501][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:45.502][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:45.503][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.504][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.505][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.506][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-09-09 13:54:45.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.527][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-09-09 13:54:45.528][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:45.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:45.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:45.535][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:45.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.546][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:45.547][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-09-09 13:54:45.547][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-09-09 13:54:45.548][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-09-09 13:54:45.549][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:45.550][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.551][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.552][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.553][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.554][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.555][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.556][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.556][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:45.557][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:45.558][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.559][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.560][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.561][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-09-09 13:54:45.562][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.573][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-09-09 13:54:45.574][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:45.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:45.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:45.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.583][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:45.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.592][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:45.592][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-09-09 13:54:45.593][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-09-09 13:54:45.594][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-09-09 13:54:45.595][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:45.596][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.597][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.598][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.599][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.600][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.601][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.602][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:45.603][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:45.604][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.605][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.605][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.606][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.607][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-09-09 13:54:45.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:45.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.618][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-09-09 13:54:45.619][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-09-09 13:54:45.620][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-09-09 13:54:45.631][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:45.642][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:45.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:45.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:45.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:45.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:45.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:45.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:45.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:45.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:45.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:45.713][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:45.717][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:45.718][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:45.720][private$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[2025-09-09 13:54:45.796][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[2025-09-09 13:54:45.868][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:45.870][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-09-09 13:54:45.875][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-09-09 13:54:45.890][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[2025-09-09 13:54:45.893][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:45.894][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:45.896][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-09 13:54:45.974][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-09-09 13:54:46.046][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:46.049][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-09-09 13:54:46.053][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-09-09 13:54:46.057][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:46.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:46.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:46.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:46.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:46.066][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:46.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:46.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:46.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:46.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:46.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:46.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:46.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:46.088][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:46.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:46.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.097][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:46.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:46.101][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:46.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:46.107][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:46.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:46.109][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:46.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:46.111][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:46.146][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-09-09 13:54:46.173][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:46.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:46.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:46.184][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:46.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:46.186][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:46.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:46.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.198][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.199][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-09-09 13:54:46.199][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-09-09 13:54:46.200][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-09-09 13:54:46.201][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.202][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.203][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.204][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.204][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.205][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.206][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.207][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.208][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.208][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.209][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.210][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.211][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.212][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.213][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.213][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-09-09 13:54:46.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.230][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-09-09 13:54:46.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:46.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:46.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:46.239][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:46.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:46.241][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:46.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:46.255][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.287][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.288][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-09-09 13:54:46.289][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-09-09 13:54:46.290][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-09-09 13:54:46.291][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.292][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.294][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.296][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.297][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.299][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.300][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.301][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.302][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.303][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.314][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.315][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.316][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.318][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.319][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-09-09 13:54:46.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.323][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.330][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-09-09 13:54:46.331][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:46.332][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:46.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:46.338][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:46.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:46.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:46.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:46.342][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.349][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.351][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-09-09 13:54:46.354][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-09-09 13:54:46.355][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-09-09 13:54:46.356][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.357][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.358][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.358][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.359][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.360][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.361][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.362][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.362][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.363][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.364][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.365][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.366][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.367][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.367][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.368][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-09-09 13:54:46.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.391][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-09-09 13:54:46.393][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-09-09 13:54:46.394][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-09-09 13:54:46.404][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-09-09 13:54:46.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-09-09 13:54:46.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-09-09 13:54:46.412][biodb::testThat]
biodb.INFO [2025-09-09 13:54:46.413][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-09-09 13:54:46.414][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:54:46.415][biodb::testThat]
biodb.TRACE[2025-09-09 13:54:46.418][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-09 13:54:46.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-09 13:54:46.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.425][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.428][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.432][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:46.438][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:46.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:46.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:46.446][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:46.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:46.448][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:46.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:46.452][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:46.456][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:46.457][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-09-09 13:54:46.458][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:46.460][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-09-09 13:54:46.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:46.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:46.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:46.469][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:46.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:46.471][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:46.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:46.473][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.479][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.483][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:46.487][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:46.491][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:46.492][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-09-09 13:54:46.493][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:46.495][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-09-09 13:54:46.497][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:46.498][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:46.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:46.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:46.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:46.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:46.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:46.509][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.513][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.516][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:46.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:46.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:46.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:46.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:46.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:46.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:46.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:46.530][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.537][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:46.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:46.540][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-09-09 13:54:46.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:46.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:46.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:46.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:46.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:46.551][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:46.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:46.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.559][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.560][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-09-09 13:54:46.561][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-09-09 13:54:46.562][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-09-09 13:54:46.563][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.563][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.564][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.566][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.567][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.568][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.569][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.569][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.570][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.571][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.572][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.573][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.575][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.576][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-09-09 13:54:46.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.587][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-09-09 13:54:46.588][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:46.589][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:46.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:46.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:46.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:46.600][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:46.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:46.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.609][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.610][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-09-09 13:54:46.611][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-09-09 13:54:46.611][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-09-09 13:54:46.613][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.615][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.616][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.618][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.619][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.620][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.621][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.622][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.623][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.624][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.624][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.625][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.626][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.628][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.629][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-09-09 13:54:46.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.641][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-09-09 13:54:46.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:46.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:46.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:46.650][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:46.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:46.651][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:46.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:46.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.657][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.660][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.661][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-09-09 13:54:46.662][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-09-09 13:54:46.663][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-09-09 13:54:46.663][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.664][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.665][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.667][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.667][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.668][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.670][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.671][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.671][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.672][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.673][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.674][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.675][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.675][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-09-09 13:54:46.676][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.680][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.687][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-09-09 13:54:46.688][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-09-09 13:54:46.688][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-09-09 13:54:46.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.710][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:46.719][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:46.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:46.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:46.727][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:46.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:46.729][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:46.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:46.733][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:46.736][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:46.738][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-09-09 13:54:46.746][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:46.749][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-09-09 13:54:46.753][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:46.757][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:46.758][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-09-09 13:54:46.759][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:46.761][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-09-09 13:54:46.763][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:46.764][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:46.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:46.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:46.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:46.772][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:46.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:46.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.778][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:46.784][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:46.785][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:46.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:46.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:46.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:46.793][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:46.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:46.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.803][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:46.806][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:46.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:46.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:46.814][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:46.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:46.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:46.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:46.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:46.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:46.833][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-09-09 13:54:46.835][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:46.836][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:46.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:46.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:46.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:46.845][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:46.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:46.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.854][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.855][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-09-09 13:54:46.856][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-09-09 13:54:46.856][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-09-09 13:54:46.857][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.858][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.859][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.860][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.861][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.862][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.864][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.865][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.866][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.867][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.869][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.869][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.870][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.871][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.872][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.873][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-09-09 13:54:46.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.883][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.887][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-09-09 13:54:46.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:46.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:46.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:46.895][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:46.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:46.897][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:46.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:46.899][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.906][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.907][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-09-09 13:54:46.908][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-09-09 13:54:46.908][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-09-09 13:54:46.909][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.910][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.911][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.912][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.913][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.914][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.915][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.916][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.917][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.918][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.918][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.919][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.920][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.921][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.922][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-09-09 13:54:46.922][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.926][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.929][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.932][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-09-09 13:54:46.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:46.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:46.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:46.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:46.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:46.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:46.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:46.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.955][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.956][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-09-09 13:54:46.957][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-09-09 13:54:46.958][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-09-09 13:54:46.958][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.959][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.960][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.962][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.963][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.964][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.965][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.966][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.967][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:46.968][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.969][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.970][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.971][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-09-09 13:54:46.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.975][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.978][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:46.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:46.982][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-09-09 13:54:46.983][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-09-09 13:54:46.984][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-09-09 13:54:46.993][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-09-09 13:54:46.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-09-09 13:54:46.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:46.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-09-09 13:54:47.001][biodb::testThat]
biodb.INFO [2025-09-09 13:54:47.002][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-09-09 13:54:47.003][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:54:47.003][biodb::testThat]
biodb.TRACE[2025-09-09 13:54:47.007][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-09 13:54:47.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-09 13:54:47.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.010][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.013][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.017][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.020][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:47.029][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:47.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:47.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:47.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:47.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:47.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:47.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:47.044][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:47.048][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:47.049][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-09-09 13:54:47.051][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:47.052][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-09-09 13:54:47.055][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:47.056][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:47.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:47.062][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:47.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:47.064][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:47.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:47.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.070][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:47.080][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:47.083][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:47.085][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-09-09 13:54:47.086][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:47.087][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-09-09 13:54:47.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:47.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:47.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:47.097][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:47.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:47.099][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:47.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:47.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:47.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:47.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:47.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:47.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:47.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:47.127][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:47.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:47.129][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:47.139][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-09-09 13:54:47.141][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:47.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:47.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:47.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:47.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:47.149][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:47.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:47.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.158][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.159][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-09-09 13:54:47.159][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-09-09 13:54:47.160][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-09-09 13:54:47.161][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.162][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.163][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.164][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.165][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.166][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.167][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.168][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.169][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.170][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.171][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.172][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.173][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-09-09 13:54:47.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.184][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-09-09 13:54:47.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:47.186][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:47.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:47.192][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:47.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:47.194][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:47.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:47.196][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.203][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.203][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-09-09 13:54:47.204][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-09-09 13:54:47.205][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-09-09 13:54:47.206][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.207][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.208][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.209][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.210][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.211][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.212][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.213][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.213][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.214][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.215][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.216][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.217][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.217][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.218][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-09-09 13:54:47.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.229][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-09-09 13:54:47.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:47.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:47.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:47.237][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:47.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:47.239][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:47.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:47.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.247][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.248][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-09-09 13:54:47.249][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-09-09 13:54:47.250][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-09-09 13:54:47.251][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.252][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.253][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.254][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.255][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.256][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.258][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.258][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.259][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.260][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.261][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.262][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.263][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-09-09 13:54:47.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.275][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-09-09 13:54:47.276][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-09-09 13:54:47.276][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-09-09 13:54:47.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.307][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:47.315][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:47.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:47.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:47.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:47.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:47.324][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:47.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:47.327][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:47.331][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:47.332][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-09-09 13:54:47.334][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:47.335][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-09-09 13:54:47.338][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:47.342][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:47.343][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-09-09 13:54:47.345][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:47.346][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-09-09 13:54:47.350][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:47.351][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:47.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:47.357][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:47.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:47.359][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:47.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:47.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:47.371][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:47.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:47.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:47.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:47.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:47.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:47.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:47.381][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.384][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:47.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:47.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:47.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:47.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:47.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:47.400][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:47.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:47.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.405][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:47.412][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-09-09 13:54:47.414][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:47.415][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:47.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:47.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:47.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:47.422][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:47.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:47.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.431][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.432][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-09-09 13:54:47.433][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-09-09 13:54:47.433][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-09-09 13:54:47.434][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.435][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.436][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.437][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.438][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.446][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.447][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.449][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.449][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.450][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.451][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.452][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.453][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.454][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-09-09 13:54:47.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.458][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.465][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-09-09 13:54:47.466][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:47.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:47.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:47.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:47.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:47.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:47.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:47.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.484][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.485][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-09-09 13:54:47.485][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-09-09 13:54:47.486][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-09-09 13:54:47.487][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.488][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.488][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.489][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.490][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.491][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.492][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.493][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.494][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.495][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.496][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.496][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.497][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.498][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.499][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-09-09 13:54:47.500][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.503][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.510][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-09-09 13:54:47.511][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:47.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:47.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:47.518][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:47.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:47.519][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:47.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:47.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.528][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.529][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-09-09 13:54:47.529][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-09-09 13:54:47.530][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-09-09 13:54:47.531][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.532][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.533][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.534][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.534][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.535][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.536][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.538][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.539][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.540][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-09-09 13:54:47.541][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.542][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.544][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.545][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-09-09 13:54:47.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.556][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-09-09 13:54:47.557][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-09-09 13:54:47.558][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-09-09 13:54:47.578][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-09-09 13:54:47.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-09-09 13:54:47.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-09-09 13:54:47.585][biodb::testThat]
biodb.INFO [2025-09-09 13:54:47.586][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-09-09 13:54:47.587][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:54:47.588][biodb::testThat]
biodb.DEBUG[2025-09-09 13:54:47.590][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-09-09 13:54:47.591][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:47.592][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-09-09 13:54:47.593][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-09-09 13:54:47.594][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-09-09 13:54:47.595][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:47.596][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:47.597][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:47.598][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:47.601][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:47.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:47.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:47.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:47.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:47.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:47.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:47.612][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-09-09 13:54:47.615][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:47.616][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:47.618][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-09-09 13:54:47.696][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-09-09 13:54:47.774][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:47.777][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-09-09 13:54:47.780][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-09-09 13:54:47.783][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-09-09 13:54:47.784][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:47.786][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:47.787][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:47.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:47.789][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:47.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:47.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:47.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:47.797][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:47.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:47.800][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:47.801][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:47.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.802][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:47.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:47.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.807][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:47.808][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:47.809][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.809][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.810][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:47.811][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:47.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.813][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.814][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:47.815][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:47.816][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.817][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.817][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:47.818][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:47.819][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.820][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.821][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:47.822][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:47.823][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.823][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.824][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:47.825][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:47.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.827][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.828][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.828][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:47.829][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.830][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.831][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:47.832][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:47.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.833][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.834][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:47.835][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:47.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.837][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.838][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:47.839][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:47.839][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.840][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.844][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:47.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:47.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:47.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:47.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:47.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:47.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:47.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:47.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:47.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:47.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:47.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:47.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:47.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:47.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:47.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:47.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:47.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:47.873][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-09-09 13:54:47.874][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-09-09 13:54:47.883][biodb::testThat]
biodb.INFO [2025-09-09 13:54:47.884][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-09-09 13:54:47.885][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:54:47.885][biodb::testThat]
biodb.DEBUG[2025-09-09 13:54:47.895][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-09-09 13:54:47.897][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-09-09 13:54:47.898][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-09-09 13:54:47.899][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-09-09 13:54:47.901][cch$loadFileContent] file.exist = [3]: "FALSE, TRUE, FALSE".
biodb.TRACE[2025-09-09 13:54:47.902][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml".
biodb.DEBUG[2025-09-09 13:54:47.903][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:47.904][conn$getEntryContent] 2 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:47.905][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-09 13:54:47.906][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-09-09 13:54:47.910][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:47.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:47.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:47.917][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:47.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:47.919][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:47.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:47.921][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-09-09 13:54:47.935][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:47.936][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:47.937][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-09-09 13:54:48.013][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-09-09 13:54:48.090][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:48.092][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-09-09 13:54:48.095][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-09-09 13:54:48.097][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:48.098][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:48.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:48.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:48.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:48.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:48.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:48.108][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-09-09 13:54:48.110][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:48.111][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:48.113][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-09-09 13:54:48.197][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-09-09 13:54:48.276][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:48.278][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-09-09 13:54:48.283][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-09-09 13:54:48.286][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-09-09 13:54:48.288][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-09-09 13:54:48.289][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-09-09 13:54:48.290][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:48.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:48.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:48.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:48.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:48.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:48.302][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:48.303][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.TRACE[2025-09-09 13:54:48.305][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.307][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.310][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.317][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:48.318][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:48.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.319][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.321][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:48.322][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:48.323][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.323][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.325][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:48.326][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:48.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.327][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.328][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:48.329][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:48.330][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.331][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.332][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:48.333][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:48.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.334][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.336][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:48.336][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:48.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.338][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.339][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:48.340][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:48.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.342][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.343][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:48.344][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:48.345][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.345][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.347][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:48.347][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:48.348][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.349][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.350][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:48.351][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:48.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.353][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.354][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:48.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:48.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.358][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:48.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:48.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.365][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:48.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:48.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:48.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:48.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:48.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:48.386][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:48.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:48.388][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:48.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:48.391][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.392][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.393][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.394][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.399][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:48.400][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:48.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.402][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.403][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:48.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:48.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.407][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:48.408][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:48.409][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.410][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.412][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:48.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:48.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.415][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:48.416][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:48.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.418][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.419][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:48.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:48.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.422][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:48.423][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:48.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.425][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.426][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:48.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:48.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.429][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:48.430][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:48.431][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.432][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.433][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:48.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:48.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.437][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:48.437][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:48.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.439][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.440][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:48.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:48.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.444][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:48.444][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:48.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.446][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:48.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:48.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.451][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:48.452][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:48.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.454][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.455][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:48.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:48.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.458][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:48.459][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:48.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.461][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.462][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:48.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:48.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.465][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:48.466][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:48.467][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.468][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.469][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:48.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:48.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:48.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:48.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:48.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:48.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:48.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:48.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:48.497][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:48.498][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:48.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:48.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:48.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:48.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:48.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:48.510][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.511][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.513][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.518][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:48.519][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:48.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.520][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.521][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:48.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:48.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.526][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:48.527][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:48.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.528][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.530][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:48.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:48.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.533][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:48.534][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:48.535][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.536][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.537][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:48.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:48.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.540][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:48.541][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:48.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.543][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:48.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:48.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.548][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:48.549][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:48.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.551][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.552][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:48.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:48.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.556][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:48.557][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:48.558][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.558][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.559][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:48.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:48.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.563][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:48.564][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:48.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.566][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:48.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:48.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.570][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:48.571][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:48.572][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.572][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.574][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:48.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:48.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.591][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:48.591][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:48.592][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.593][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.594][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:48.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:48.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.598][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:48.599][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:48.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.600][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.601][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:48.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:48.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:48.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:48.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:48.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:48.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:48.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:48.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:48.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:48.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:48.659][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-09-09 13:54:48.661][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-09-09 13:54:48.662][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-09-09 13:54:48.678][biodb::testThat]
biodb.INFO [2025-09-09 13:54:48.679][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-09-09 13:54:48.680][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:54:48.681][biodb::testThat]
biodb.INFO [2025-09-09 13:54:48.707][biodb::testThat]
biodb.INFO [2025-09-09 13:54:48.708][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-09-09 13:54:48.709][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:54:48.710][biodb::testThat]
biodb.INFO [2025-09-09 13:54:48.718][biodb::testThat]
biodb.INFO [2025-09-09 13:54:48.719][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-09-09 13:54:48.720][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:54:48.721][biodb::testThat]
biodb.DEBUG[2025-09-09 13:54:48.723][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[2025-09-09 13:54:48.727][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:48.728][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:48.730][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-09-09 13:54:48.861][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-09-09 13:54:48.967][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:48.970][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-09-09 13:54:48.975][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-09-09 13:54:48.988][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:48.989][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:48.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.991][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:48.992][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:48.993][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:48.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:48.994][ef$get] fields variable is a list.
biodb.INFO [2025-09-09 13:54:48.996][biodb::testThat]
biodb.INFO [2025-09-09 13:54:48.997][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2025-09-09 13:54:48.998][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:54:48.999][biodb::testThat]
biodb.ERROR[2025-09-09 13:54:49.012][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-09-09 13:54:49.028][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-09-09 13:54:49.041][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-09-09 13:54:49.042][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-09-09 13:54:49.043][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-09-09 13:54:49.044][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-09 13:54:49.045][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.046][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.048][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-09-09 13:54:49.059][biodb::testContext]
biodb.INFO [2025-09-09 13:54:49.060][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-09 13:54:49.061][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-09-09 13:54:49.062][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-09 13:54:49.063][biodb::testContext]
biodb.INFO [2025-09-09 13:54:49.065][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-09-09 13:54:49.067][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-09-09 13:54:49.072][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-09 13:54:49.073][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-09 13:54:49.074][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-09 13:54:49.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.077][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-09 13:54:49.078][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-09 13:54:49.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.081][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-09 13:54:49.082][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-09 13:54:49.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.085][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-09 13:54:49.085][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-09 13:54:49.086][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-09 13:54:49.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.089][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-09 13:54:49.090][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-09 13:54:49.091][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-09 13:54:49.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.094][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-09 13:54:49.095][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-09 13:54:49.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.098][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-09 13:54:49.099][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-09 13:54:49.099][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-09 13:54:49.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.102][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-09 13:54:49.103][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-09 13:54:49.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.106][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-09 13:54:49.107][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-09 13:54:49.108][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-09 13:54:49.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.111][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-09 13:54:49.112][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-09 13:54:49.113][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-09 13:54:49.113][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-09 13:54:49.114][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-09 13:54:49.115][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-09 13:54:49.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.118][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-09 13:54:49.119][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-09 13:54:49.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.122][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-09 13:54:49.123][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-09 13:54:49.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.126][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-09 13:54:49.127][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-09 13:54:49.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.130][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-09 13:54:49.130][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-09-09 13:54:49.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.133][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-09 13:54:49.134][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-09 13:54:49.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.137][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-09 13:54:49.138][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-09 13:54:49.155][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-09 13:54:49.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.159][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-09 13:54:49.160][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-09 13:54:49.161][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-09 13:54:49.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.165][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-09 13:54:49.177][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:49.178][self$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[2025-09-09 13:54:49.179][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:49.180][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-09 13:54:49.181][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:49.182][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-09 13:54:49.183][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:49.183][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-09 13:54:49.184][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-09 13:54:49.185][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-09 13:54:49.186][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:49.187][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-09 13:54:49.188][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-09 13:54:49.189][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:49.190][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:49.191][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-09 13:54:49.191][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-09 13:54:49.191][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-09 13:54:49.191][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-09 13:54:49.191][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-09 13:54:49.192][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-09 13:54:49.193][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:49.194][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:49.195][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-09 13:54:49.196][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:49.196][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:49.197][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-09 13:54:49.198][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:49.199][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-09 13:54:49.199][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-09 13:54:49.200][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:49.201][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:49.202][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-09 13:54:49.204][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:49.205][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-09 13:54:49.206][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:49.207][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-09 13:54:49.208][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:49.208][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-09 13:54:49.209][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:49.210][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-09 13:54:49.211][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-09 13:54:49.212][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-09 13:54:49.213][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:49.213][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-09 13:54:49.214][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-09 13:54:49.215][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:49.216][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:49.217][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-09 13:54:49.217][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-09 13:54:49.217][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-09 13:54:49.217][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-09 13:54:49.217][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-09 13:54:49.218][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-09 13:54:49.218][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:49.219][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:49.220][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-09 13:54:49.221][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:49.222][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:49.222][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-09 13:54:49.223][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:49.224][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-09 13:54:49.225][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-09 13:54:49.226][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:49.227][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:49.228][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-09 13:54:49.230][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:49.231][self$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[2025-09-09 13:54:49.232][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:49.233][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-09 13:54:49.233][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:49.234][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-09 13:54:49.235][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:49.236][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-09 13:54:49.237][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-09 13:54:49.238][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-09 13:54:49.238][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:49.239][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-09 13:54:49.240][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-09 13:54:49.241][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:49.242][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:49.243][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:49.243][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-09 13:54:49.244][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:49.245][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:49.246][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-09 13:54:49.247][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:49.247][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:49.248][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-09 13:54:49.249][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:49.250][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-09 13:54:49.250][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-09 13:54:49.251][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:49.252][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:49.253][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-09 13:54:49.255][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:49.256][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-09 13:54:49.257][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:49.257][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-09 13:54:49.258][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:49.259][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-09 13:54:49.260][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:49.261][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-09 13:54:49.262][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-09 13:54:49.262][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-09 13:54:49.263][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:49.264][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-09 13:54:49.265][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-09 13:54:49.266][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:49.267][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:49.267][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:49.268][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-09 13:54:49.269][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:49.270][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:49.271][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-09 13:54:49.272][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:49.273][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:49.274][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-09 13:54:49.274][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:49.275][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-09 13:54:49.276][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-09 13:54:49.277][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:49.278][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:49.279][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-09 13:54:49.280][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.281][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[2025-09-09 13:54:49.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.284][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[2025-09-09 13:54:49.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.288][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[2025-09-09 13:54:49.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.291][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[2025-09-09 13:54:49.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.299][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[2025-09-09 13:54:49.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.306][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.DEBUG[2025-09-09 13:54:49.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.329][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[2025-09-09 13:54:49.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.333][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[2025-09-09 13:54:49.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.337][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[2025-09-09 13:54:49.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.340][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[2025-09-09 13:54:49.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.345][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-09 13:54:49.346][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-09 13:54:49.347][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-09 13:54:49.348][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-09 13:54:49.350][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-09 13:54:49.351][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-09 13:54:49.352][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-09 13:54:49.353][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-09 13:54:49.354][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-09 13:54:49.356][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-09 13:54:49.357][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-09 13:54:49.358][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-09 13:54:49.359][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-09 13:54:49.360][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-09 13:54:49.361][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-09 13:54:49.363][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-09 13:54:49.364][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-09 13:54:49.365][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-09 13:54:49.366][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-09 13:54:49.368][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-09 13:54:49.369][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-09 13:54:49.370][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-09 13:54:49.371][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-09 13:54:49.372][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-09 13:54:49.374][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-09 13:54:49.375][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-09 13:54:49.376][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-09 13:54:49.377][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-09 13:54:49.378][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-09 13:54:49.379][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-09 13:54:49.381][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-09 13:54:49.382][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-09 13:54:49.383][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-09 13:54:49.384][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-09 13:54:49.386][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-09 13:54:49.387][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-09 13:54:49.388][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-09 13:54:49.389][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-09 13:54:49.391][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-09 13:54:49.392][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-09 13:54:49.393][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-09 13:54:49.395][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-09 13:54:49.396][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-09 13:54:49.397][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-09 13:54:49.398][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-09 13:54:49.399][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-09 13:54:49.401][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-09 13:54:49.402][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-09 13:54:49.403][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-09 13:54:49.404][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-09 13:54:49.405][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-09 13:54:49.407][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-09 13:54:49.408][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-09 13:54:49.409][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-09 13:54:49.410][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-09 13:54:49.411][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-09 13:54:49.412][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-09 13:54:49.414][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-09 13:54:49.415][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-09 13:54:49.416][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-09 13:54:49.417][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-09 13:54:49.418][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-09 13:54:49.419][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-09 13:54:49.421][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-09 13:54:49.422][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-09 13:54:49.423][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-09 13:54:49.424][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-09 13:54:49.425][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-09 13:54:49.426][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-09 13:54:49.428][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-09 13:54:49.429][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-09 13:54:49.430][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-09 13:54:49.431][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-09 13:54:49.433][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-09 13:54:49.434][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-09 13:54:49.435][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-09 13:54:49.436][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-09 13:54:49.438][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-09 13:54:49.439][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-09 13:54:49.440][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-09 13:54:49.441][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-09 13:54:49.442][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-09 13:54:49.444][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-09 13:54:49.445][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-09 13:54:49.447][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-09-09 13:54:49.448][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-09 13:54:49.449][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.451][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.451][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[2025-09-09 13:54:49.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.457][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[2025-09-09 13:54:49.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.463][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[2025-09-09 13:54:49.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.517][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[2025-09-09 13:54:49.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.528][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[2025-09-09 13:54:49.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:49.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.550][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-09-09 13:54:49.552][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-09-09 13:54:49.554][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:49.555][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-09-09 13:54:49.556][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:49.556][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-09 13:54:49.557][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:49.558][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-09 13:54:49.559][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:49.560][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-09-09 13:54:49.561][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-09 13:54:49.562][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-09 13:54:49.563][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:49.563][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-09-09 13:54:49.564][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-09 13:54:49.565][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-09-09 13:54:49.565][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-09-09 13:54:49.565][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-09-09 13:54:49.565][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-09-09 13:54:49.565][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-09-09 13:54:49.565][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-09-09 13:54:49.565][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-09-09 13:54:49.565][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-09-09 13:54:49.565][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-09-09 13:54:49.565][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-09-09 13:54:49.565][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-09-09 13:54:49.566][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:49.567][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-09 13:54:49.567][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-09 13:54:49.567][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-09 13:54:49.569][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-09 13:54:49.570][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:49.571][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:49.572][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-09 13:54:49.573][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:49.573][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:49.574][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-09 13:54:49.575][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:49.575][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-09-09 13:54:49.576][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-09 13:54:49.577][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-09 13:54:49.577][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:49.578][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-09-09 13:54:49.578][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-09-09 13:54:49.579][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-09 13:54:49.581][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-09 13:54:49.582][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-09-09 13:54:49.584][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-09 13:54:49.585][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-09 13:54:49.586][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-09 13:54:49.589][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-09-09 13:54:49.591][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-09-09 13:54:49.592][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-09-09 13:54:49.594][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-09-09 13:54:49.595][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-09-09 13:54:49.596][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-09-09 13:54:49.597][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-09-09 13:54:49.598][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-09-09 13:54:49.600][biodb::testThat]
biodb.INFO [2025-09-09 13:54:49.600][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2025-09-09 13:54:49.601][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:54:49.602][biodb::testThat]
biodb.DEBUG[2025-09-09 13:54:49.606][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-09-09 13:54:49.610][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:49.611][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-09-09 13:54:49.612][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:49.614][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-09-09 13:54:49.618][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:49.622][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:49.623][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-09-09 13:54:49.624][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:49.626][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-09-09 13:54:49.628][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:49.629][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.637][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.639][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:49.643][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:49.644][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-09-09 13:54:49.646][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:49.647][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-09-09 13:54:49.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:49.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:49.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.683][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.685][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.685][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[2025-09-09 13:54:49.690][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:49.694][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:49.695][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-09-09 13:54:49.696][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:49.697][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-09-09 13:54:49.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:49.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.710][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:49.713][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:49.715][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-09-09 13:54:49.716][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:49.717][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-09-09 13:54:49.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:49.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.727][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.729][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.729][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[2025-09-09 13:54:49.730][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:49.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.738][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.743][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:49.746][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:49.747][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-09-09 13:54:49.749][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:49.750][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-09-09 13:54:49.751][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:49.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.758][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.760][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.762][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:49.765][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:49.767][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-09-09 13:54:49.768][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:49.769][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-09-09 13:54:49.771][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:49.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.779][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:49.782][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:49.785][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:49.786][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2025-09-09 13:54:49.787][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:49.789][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2025-09-09 13:54:49.790][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:49.791][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:49.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:49.797][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:49.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:49.799][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:49.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-09-09 13:54:49.813][biodb::testThat]
biodb.INFO [2025-09-09 13:54:49.814][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2025-09-09 13:54:49.815][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:54:49.816][biodb::testThat]
biodb.DEBUG[2025-09-09 13:54:49.819][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:49.823][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:49.824][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:49.825][private$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[2025-09-09 13:54:49.930][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[2025-09-09 13:54:50.001][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:50.004][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-09-09 13:54:50.008][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-09-09 13:54:50.011][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:50.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:50.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:50.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.021][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.DEBUG[2025-09-09 13:54:50.025][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[2025-09-09 13:54:50.029][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-09 13:54:50.030][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-09 13:54:50.045][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-09-09 13:54:50.118][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-09-09 13:54:50.195][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-09-09 13:54:50.198][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-09-09 13:54:50.202][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-09-09 13:54:50.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:50.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:50.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:50.212][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.214][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-09-09 13:54:50.220][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-09-09 13:54:50.221][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-09-09 13:54:50.222][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-09-09 13:54:50.223][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-09 13:54:50.223][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:50.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:50.225][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.226][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-09-09 13:54:50.231][biodb::testContext]
biodb.INFO [2025-09-09 13:54:50.232][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-09 13:54:50.233][biodb::testContext] Test context - Test web services
biodb.INFO [2025-09-09 13:54:50.233][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-09 13:54:50.234][biodb::testContext]
biodb.INFO [2025-09-09 13:54:50.237][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-09-09 13:54:50.238][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-09-09 13:54:50.243][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-09 13:54:50.244][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-09 13:54:50.245][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-09 13:54:50.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.248][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-09 13:54:50.249][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-09 13:54:50.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.252][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-09 13:54:50.253][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-09 13:54:50.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.255][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[2025-09-09 13:54:50.256][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-09 13:54:50.257][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-09 13:54:50.258][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-09 13:54:50.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.261][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-09 13:54:50.262][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-09 13:54:50.263][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-09 13:54:50.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.266][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-09 13:54:50.267][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-09 13:54:50.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.270][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-09 13:54:50.271][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-09 13:54:50.272][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-09 13:54:50.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.275][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-09 13:54:50.275][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-09 13:54:50.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.278][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-09 13:54:50.279][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-09 13:54:50.280][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-09 13:54:50.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.282][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[2025-09-09 13:54:50.283][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-09 13:54:50.284][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-09 13:54:50.285][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-09 13:54:50.286][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-09 13:54:50.286][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-09 13:54:50.287][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-09 13:54:50.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.290][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-09 13:54:50.291][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-09 13:54:50.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.294][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-09 13:54:50.295][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-09 13:54:50.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.298][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-09 13:54:50.299][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-09 13:54:50.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.302][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-09 13:54:50.303][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-09-09 13:54:50.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.306][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-09 13:54:50.307][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-09 13:54:50.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.310][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-09 13:54:50.311][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-09 13:54:50.329][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-09 13:54:50.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.333][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-09 13:54:50.334][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-09 13:54:50.335][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-09 13:54:50.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.337][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[2025-09-09 13:54:50.338][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-09 13:54:50.340][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:50.341][self$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[2025-09-09 13:54:50.342][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.343][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-09 13:54:50.344][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.345][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-09 13:54:50.345][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:50.346][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-09 13:54:50.347][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-09 13:54:50.348][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-09 13:54:50.349][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.350][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-09 13:54:50.350][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-09 13:54:50.351][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:50.352][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.353][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-09 13:54:50.353][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-09 13:54:50.353][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-09 13:54:50.353][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-09 13:54:50.353][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-09 13:54:50.354][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-09 13:54:50.355][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:50.356][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:50.356][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-09 13:54:50.357][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:50.358][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:50.359][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-09 13:54:50.360][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:50.360][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-09 13:54:50.361][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-09 13:54:50.362][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:50.363][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:50.364][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-09 13:54:50.366][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:50.366][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-09 13:54:50.367][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.368][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-09 13:54:50.369][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.370][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-09 13:54:50.371][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:50.371][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-09 13:54:50.372][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-09 13:54:50.373][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-09 13:54:50.374][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.375][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-09 13:54:50.376][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-09 13:54:50.376][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:50.377][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.378][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-09 13:54:50.378][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-09 13:54:50.378][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-09 13:54:50.378][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-09 13:54:50.378][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-09 13:54:50.379][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-09 13:54:50.380][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:50.381][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:50.381][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-09 13:54:50.382][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:50.383][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:50.384][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-09 13:54:50.385][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:50.385][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-09 13:54:50.386][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-09 13:54:50.387][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:50.388][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:50.389][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-09 13:54:50.390][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.391][self$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[2025-09-09 13:54:50.392][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.393][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-09 13:54:50.394][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.395][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-09 13:54:50.395][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:50.396][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-09 13:54:50.397][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-09 13:54:50.398][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-09 13:54:50.399][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:50.399][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-09 13:54:50.400][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-09 13:54:50.401][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:50.402][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.403][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:50.403][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-09 13:54:50.404][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:50.405][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:50.406][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-09 13:54:50.407][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:50.407][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:50.408][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-09 13:54:50.409][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:50.410][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-09 13:54:50.410][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-09 13:54:50.411][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:50.412][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:50.413][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-09 13:54:50.415][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.416][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-09 13:54:50.417][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.417][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-09 13:54:50.418][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.419][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-09 13:54:50.420][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:50.421][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-09 13:54:50.421][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-09 13:54:50.422][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-09 13:54:50.423][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:50.424][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-09 13:54:50.425][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-09 13:54:50.425][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:50.426][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.427][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:50.428][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-09 13:54:50.429][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:50.429][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:50.430][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-09 13:54:50.431][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:50.432][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:50.433][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-09 13:54:50.434][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:50.434][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-09 13:54:50.435][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-09 13:54:50.436][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:50.437][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:50.438][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-09 13:54:50.439][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.439][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[2025-09-09 13:54:50.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.443][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[2025-09-09 13:54:50.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.466][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[2025-09-09 13:54:50.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.477][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[2025-09-09 13:54:50.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.494][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[2025-09-09 13:54:50.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.516][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[2025-09-09 13:54:50.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.521][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[2025-09-09 13:54:50.522][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-09 13:54:50.523][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-09 13:54:50.524][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-09 13:54:50.526][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-09 13:54:50.528][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-09 13:54:50.529][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-09 13:54:50.531][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-09 13:54:50.532][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-09 13:54:50.534][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-09 13:54:50.535][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-09 13:54:50.537][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-09 13:54:50.539][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-09 13:54:50.540][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-09 13:54:50.542][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-09 13:54:50.544][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-09 13:54:50.546][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-09 13:54:50.547][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-09 13:54:50.549][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-09 13:54:50.550][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-09 13:54:50.551][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-09 13:54:50.552][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-09 13:54:50.553][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-09 13:54:50.555][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-09 13:54:50.556][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-09 13:54:50.558][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-09 13:54:50.560][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-09 13:54:50.561][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-09 13:54:50.563][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-09 13:54:50.564][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-09 13:54:50.565][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-09 13:54:50.566][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-09 13:54:50.568][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-09 13:54:50.569][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-09 13:54:50.571][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-09 13:54:50.573][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-09 13:54:50.574][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-09 13:54:50.576][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-09 13:54:50.577][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-09 13:54:50.578][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-09 13:54:50.580][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-09 13:54:50.581][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-09 13:54:50.582][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-09 13:54:50.584][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-09 13:54:50.585][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-09 13:54:50.586][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-09 13:54:50.587][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-09 13:54:50.589][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-09 13:54:50.590][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-09 13:54:50.591][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-09 13:54:50.592][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-09 13:54:50.593][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-09 13:54:50.595][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-09 13:54:50.596][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-09 13:54:50.597][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-09 13:54:50.599][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-09 13:54:50.600][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-09 13:54:50.601][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-09 13:54:50.602][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-09 13:54:50.603][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-09 13:54:50.605][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-09 13:54:50.606][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-09 13:54:50.608][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-09 13:54:50.609][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-09 13:54:50.611][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-09 13:54:50.614][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-09 13:54:50.615][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-09 13:54:50.617][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-09 13:54:50.619][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-09 13:54:50.620][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-09 13:54:50.622][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-09 13:54:50.624][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-09 13:54:50.625][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-09 13:54:50.626][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-09 13:54:50.627][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-09 13:54:50.629][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-09 13:54:50.630][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-09 13:54:50.631][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-09 13:54:50.632][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-09 13:54:50.633][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-09 13:54:50.635][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-09 13:54:50.636][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-09 13:54:50.637][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-09 13:54:50.638][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-09 13:54:50.639][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-09 13:54:50.641][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-09-09 13:54:50.642][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-09 13:54:50.643][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.645][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:50.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:50.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:50.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:50.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:50.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:50.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:50.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:50.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:50.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:50.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:50.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:50.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:50.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:50.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.684][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[2025-09-09 13:54:50.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:50.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:50.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.690][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[2025-09-09 13:54:50.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:50.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:50.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:50.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:50.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:50.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:50.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:50.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:50.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.716][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[2025-09-09 13:54:50.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:50.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:50.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:50.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:50.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:50.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:50.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.732][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[2025-09-09 13:54:50.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:50.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:50.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:50.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:50.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.742][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[2025-09-09 13:54:50.745][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-09-09 13:54:50.747][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-09-09 13:54:50.749][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:50.750][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-09-09 13:54:50.751][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.752][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-09 13:54:50.753][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.754][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-09 13:54:50.755][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.756][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-09-09 13:54:50.757][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-09 13:54:50.758][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-09 13:54:50.759][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.760][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-09-09 13:54:50.760][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-09 13:54:50.761][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-09-09 13:54:50.761][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-09-09 13:54:50.761][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-09-09 13:54:50.761][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-09-09 13:54:50.761][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-09-09 13:54:50.761][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-09-09 13:54:50.761][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-09-09 13:54:50.761][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-09-09 13:54:50.761][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-09-09 13:54:50.761][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-09-09 13:54:50.761][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-09-09 13:54:50.763][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:50.764][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-09 13:54:50.764][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-09 13:54:50.764][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-09 13:54:50.765][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-09 13:54:50.766][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:50.766][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:50.767][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-09 13:54:50.768][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:50.769][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:50.770][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-09 13:54:50.771][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:50.771][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-09-09 13:54:50.771][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-09 13:54:50.772][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-09 13:54:50.773][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.774][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-09-09 13:54:50.774][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-09-09 13:54:50.775][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-09 13:54:50.777][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-09 13:54:50.778][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-09-09 13:54:50.779][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-09 13:54:50.781][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-09 13:54:50.790][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-09 13:54:50.794][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-09-09 13:54:50.795][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-09-09 13:54:50.796][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-09-09 13:54:50.797][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-09-09 13:54:50.798][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-09-09 13:54:50.799][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-09-09 13:54:50.800][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-09-09 13:54:50.801][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-09-09 13:54:50.803][biodb::testThat]
biodb.INFO [2025-09-09 13:54:50.803][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-09-09 13:54:50.804][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:54:50.805][biodb::testThat]
biodb.DEBUG[2025-09-09 13:54:50.808][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-09-09 13:54:50.812][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:50.813][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-09-09 13:54:50.815][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:50.816][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-09-09 13:54:50.820][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:50.823][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:50.825][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-09-09 13:54:50.826][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:50.828][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.INFO [2025-09-09 13:54:50.837][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-09-09 13:54:50.840][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-09-09 13:54:50.841][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-09-09 13:54:50.842][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-09 13:54:50.844][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:50.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:50.846][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:50.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:50.848][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-09-09 13:54:50.853][biodb::testContext]
biodb.INFO [2025-09-09 13:54:50.854][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-09 13:54:50.855][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-09-09 13:54:50.856][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-09 13:54:50.856][biodb::testContext]
biodb.INFO [2025-09-09 13:54:50.859][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-09-09 13:54:50.860][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-09-09 13:54:50.866][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-09 13:54:50.867][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-09 13:54:50.868][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-09 13:54:50.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.871][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-09 13:54:50.872][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-09 13:54:50.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.875][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-09 13:54:50.876][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-09 13:54:50.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.879][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-09 13:54:50.880][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-09 13:54:50.881][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-09 13:54:50.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.884][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-09 13:54:50.885][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-09 13:54:50.886][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-09 13:54:50.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.889][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-09 13:54:50.890][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-09 13:54:50.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.893][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-09 13:54:50.893][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-09 13:54:50.894][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-09 13:54:50.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.897][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-09 13:54:50.898][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-09 13:54:50.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.901][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-09 13:54:50.902][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-09 13:54:50.903][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-09 13:54:50.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.906][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-09 13:54:50.907][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-09 13:54:50.908][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-09 13:54:50.909][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-09 13:54:50.909][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-09 13:54:50.910][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-09 13:54:50.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.913][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-09 13:54:50.914][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-09 13:54:50.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.917][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-09 13:54:50.918][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-09 13:54:50.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.921][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-09 13:54:50.922][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-09 13:54:50.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.924][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.DEBUG[2025-09-09 13:54:50.925][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-09 13:54:50.925][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-09-09 13:54:50.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.929][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-09 13:54:50.929][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-09 13:54:50.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.932][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-09 13:54:50.933][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-09 13:54:50.950][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-09 13:54:50.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.953][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-09 13:54:50.954][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-09 13:54:50.955][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-09 13:54:50.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:50.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:50.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:50.959][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-09 13:54:50.960][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:50.961][self$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[2025-09-09 13:54:50.962][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.963][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-09 13:54:50.964][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.965][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-09 13:54:50.965][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:50.966][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-09 13:54:50.967][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-09 13:54:50.968][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-09 13:54:50.969][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.970][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-09 13:54:50.970][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-09 13:54:50.971][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:50.972][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.973][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-09 13:54:50.973][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-09 13:54:50.973][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-09 13:54:50.973][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-09 13:54:50.973][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-09 13:54:50.974][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-09 13:54:50.975][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:50.975][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:50.976][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-09 13:54:50.977][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:50.978][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:50.978][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-09 13:54:50.979][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:50.980][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-09 13:54:50.981][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-09 13:54:50.982][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:50.983][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:50.984][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-09 13:54:50.985][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:50.986][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-09 13:54:50.987][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.988][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-09 13:54:50.989][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.989][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-09 13:54:50.990][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:50.992][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-09 13:54:50.993][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-09 13:54:50.994][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-09 13:54:50.995][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.995][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-09 13:54:50.996][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-09 13:54:50.997][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:50.998][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:50.999][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-09 13:54:50.999][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-09 13:54:50.999][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-09 13:54:50.999][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-09 13:54:50.999][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-09 13:54:51.000][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-09 13:54:51.000][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:51.001][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:51.003][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-09 13:54:51.003][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:51.004][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:51.005][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-09 13:54:51.006][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:51.007][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-09 13:54:51.007][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-09 13:54:51.008][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:51.009][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:51.011][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-09 13:54:51.013][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:51.014][self$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[2025-09-09 13:54:51.015][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:51.016][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-09 13:54:51.016][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:51.017][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-09 13:54:51.018][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:51.019][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-09 13:54:51.020][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-09 13:54:51.021][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-09 13:54:51.022][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:51.022][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-09 13:54:51.023][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-09 13:54:51.024][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:51.025][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:51.026][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:51.027][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-09 13:54:51.027][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:51.028][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:51.029][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-09 13:54:51.030][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:51.031][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:51.031][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-09 13:54:51.032][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:51.033][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-09 13:54:51.034][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-09 13:54:51.035][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:51.035][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:51.036][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-09 13:54:51.038][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:51.039][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-09 13:54:51.040][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:51.041][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-09 13:54:51.042][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:51.043][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-09 13:54:51.043][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:51.044][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-09 13:54:51.045][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-09 13:54:51.047][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-09 13:54:51.047][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:51.048][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-09 13:54:51.049][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-09 13:54:51.050][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:51.051][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:51.052][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:51.052][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-09 13:54:51.053][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:51.054][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:51.055][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-09 13:54:51.056][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:51.056][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:51.057][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-09 13:54:51.058][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:51.059][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-09 13:54:51.059][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-09 13:54:51.060][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:51.061][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-09 13:54:51.062][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-09 13:54:51.063][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.064][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[2025-09-09 13:54:51.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.068][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[2025-09-09 13:54:51.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.071][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.DEBUG[2025-09-09 13:54:51.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.075][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[2025-09-09 13:54:51.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.131][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[2025-09-09 13:54:51.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.135][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-09 13:54:51.137][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-09 13:54:51.138][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-09 13:54:51.140][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-09 13:54:51.141][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-09 13:54:51.142][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-09 13:54:51.144][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-09 13:54:51.145][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-09 13:54:51.146][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-09 13:54:51.147][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-09 13:54:51.148][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-09 13:54:51.149][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-09 13:54:51.151][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-09 13:54:51.152][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-09 13:54:51.153][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-09 13:54:51.154][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-09 13:54:51.156][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-09 13:54:51.157][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-09 13:54:51.159][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-09 13:54:51.160][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-09 13:54:51.161][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-09 13:54:51.163][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-09 13:54:51.164][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-09 13:54:51.165][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-09 13:54:51.166][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-09 13:54:51.167][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-09 13:54:51.169][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-09 13:54:51.171][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-09 13:54:51.172][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-09 13:54:51.173][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-09 13:54:51.175][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-09 13:54:51.176][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-09 13:54:51.177][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-09 13:54:51.179][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-09 13:54:51.180][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-09 13:54:51.182][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-09 13:54:51.183][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-09 13:54:51.184][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-09 13:54:51.185][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-09 13:54:51.186][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-09 13:54:51.187][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-09 13:54:51.189][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-09 13:54:51.191][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-09 13:54:51.192][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-09 13:54:51.194][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-09 13:54:51.195][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-09 13:54:51.196][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-09 13:54:51.197][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-09 13:54:51.198][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-09 13:54:51.200][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-09 13:54:51.201][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-09 13:54:51.202][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-09 13:54:51.203][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-09 13:54:51.204][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-09 13:54:51.206][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-09 13:54:51.207][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-09 13:54:51.209][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-09 13:54:51.210][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-09 13:54:51.212][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-09 13:54:51.213][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-09 13:54:51.214][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-09 13:54:51.215][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-09 13:54:51.217][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-09 13:54:51.218][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-09 13:54:51.219][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-09 13:54:51.220][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-09 13:54:51.221][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-09 13:54:51.223][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-09 13:54:51.224][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-09 13:54:51.225][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-09 13:54:51.226][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-09 13:54:51.228][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-09 13:54:51.229][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-09 13:54:51.230][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-09 13:54:51.231][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-09 13:54:51.233][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-09 13:54:51.234][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-09 13:54:51.235][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-09 13:54:51.236][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-09 13:54:51.238][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-09 13:54:51.239][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-09 13:54:51.240][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-09 13:54:51.241][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-09 13:54:51.242][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-09 13:54:51.244][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-09-09 13:54:51.245][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-09 13:54:51.246][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.248][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.248][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.DEBUG[2025-09-09 13:54:51.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:51.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:51.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.254][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.DEBUG[2025-09-09 13:54:51.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:51.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:51.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:51.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:51.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.264][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[2025-09-09 13:54:51.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:51.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:51.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:51.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:51.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:51.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:51.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.278][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[2025-09-09 13:54:51.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:51.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:51.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:51.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:51.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:51.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:51.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:51.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:51.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:51.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:51.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.306][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.DEBUG[2025-09-09 13:54:51.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:51.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:51.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:51.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:51.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.316][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.DEBUG[2025-09-09 13:54:51.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:51.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:51.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:51.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:51.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:51.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:51.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-09 13:54:51.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:51.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:51.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-09 13:54:51.338][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-09-09 13:54:51.340][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-09-09 13:54:51.342][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:51.343][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-09-09 13:54:51.344][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:51.345][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-09 13:54:51.346][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:51.347][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-09 13:54:51.348][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:51.348][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-09-09 13:54:51.349][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-09 13:54:51.350][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-09 13:54:51.351][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:51.352][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-09-09 13:54:51.353][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-09 13:54:51.354][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-09-09 13:54:51.354][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-09-09 13:54:51.354][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-09-09 13:54:51.354][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-09-09 13:54:51.354][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-09-09 13:54:51.354][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-09-09 13:54:51.354][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-09-09 13:54:51.354][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-09-09 13:54:51.354][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-09-09 13:54:51.354][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-09-09 13:54:51.354][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-09-09 13:54:51.355][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-09 13:54:51.355][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-09 13:54:51.355][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-09 13:54:51.355][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-09 13:54:51.356][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-09 13:54:51.357][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:51.359][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:51.360][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-09 13:54:51.360][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-09 13:54:51.361][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-09 13:54:51.362][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-09 13:54:51.363][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-09 13:54:51.363][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-09-09 13:54:51.364][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-09 13:54:51.365][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-09 13:54:51.365][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-09 13:54:51.366][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-09-09 13:54:51.366][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-09-09 13:54:51.367][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-09 13:54:51.369][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-09 13:54:51.370][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-09-09 13:54:51.372][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-09 13:54:51.373][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-09 13:54:51.375][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-09 13:54:51.378][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-09-09 13:54:51.380][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-09-09 13:54:51.381][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-09-09 13:54:51.382][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-09-09 13:54:51.383][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-09-09 13:54:51.385][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-09-09 13:54:51.386][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-09-09 13:54:51.387][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-09-09 13:54:51.388][biodb::testThat]
biodb.INFO [2025-09-09 13:54:51.389][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-09-09 13:54:51.390][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-09 13:54:51.391][biodb::testThat]
biodb.DEBUG[2025-09-09 13:54:51.394][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-09-09 13:54:51.397][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:51.399][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-09-09 13:54:51.400][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:51.402][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-09-09 13:54:51.405][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-09-09 13:54:51.409][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-09 13:54:51.410][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-09-09 13:54:51.411][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:51.413][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-09-09 13:54:51.417][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-09-09 13:54:51.426][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-09 13:54:51.428][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-09-09 13:54:51.430][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-09 13:54:51.432][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml".
biodb.DEBUG[2025-09-09 13:54:51.433][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-09 13:54:51.435][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-09 13:54:51.436][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-09 13:54:51.438][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-09 13:54:51.438][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:51.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:51.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.447][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-09 13:54:51.453][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:51.455][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:51.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.456][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:51.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:51.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.461][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:51.462][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:51.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.464][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.465][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-09 13:54:51.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-09 13:54:51.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.469][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:51.470][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:51.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.471][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.473][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-09 13:54:51.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-09 13:54:51.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.476][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-09 13:54:51.477][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-09 13:54:51.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.478][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.480][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-09 13:54:51.481][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-09 13:54:51.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.482][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.484][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:51.484][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:51.485][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.486][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.487][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:51.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-09 13:54:51.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.492][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:51.493][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:51.494][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.495][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.496][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-09 13:54:51.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-09 13:54:51.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.500][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:51.501][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:51.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.504][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:51.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-09 13:54:51.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.510][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:51.511][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:51.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.513][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.514][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-09 13:54:51.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-09 13:54:51.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.518][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:51.519][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:51.520][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.521][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.522][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-09 13:54:51.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-09 13:54:51.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.525][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:51.526][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:51.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.528][ef$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.529][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-09 13:54:51.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-09 13:54:51.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:51.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:51.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:51.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:51.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:51.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:51.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.544][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-09 13:54:51.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-09 13:54:51.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:51.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:51.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:51.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:51.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:51.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:51.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:51.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:51.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:51.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:51.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-09 13:54:51.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-09 13:54:51.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-09 13:54:51.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-09 13:54:51.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-09 13:54:51.600][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-09-09 13:54:51.604][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-09-09 13:54:51.606][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-09-09 13:54:51.607][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-09-09 13:54:51.607][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-09 13:54:51.608][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-09 13:54:51.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-09 13:54:51.610][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-09 13:54:51.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-09 13:54:51.611][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-09 13:54:51.612][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 384 ]
> 
> proc.time()
   user  system elapsed 
 17.996   1.078  84.651

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn2.6121.1115.259
ChebiEntry0.3630.0180.387