Multiple platform build/check report for BioC 3.21 - CHECK results for biodbChebi on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4719
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4480
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4491
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4444
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*

CHECK results for biodbChebi on lconway

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: 1.13.0

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_1.13.0.tar.gz

StartedAt: 2025-02-05 19:10:28 -0500 (Wed, 05 Feb 2025)

EndedAt: 2025-02-05 19:13:24 -0500 (Wed, 05 Feb 2025)

EllapsedTime: 176.2 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_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck’
* using R Under development (unstable) (2025-01-22 r87618)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.13.0’
* 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 2.668  1.074   5.206
* 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-x86_64/Resources/library’
* installing *source* package ‘biodbChebi’ ...
** this is package ‘biodbChebi’ version ‘1.13.0’
** 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 Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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 [2025-02-05 19:11:27.729][biodb::testContext]
biodb.INFO [2025-02-05 19:11:27.735][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-05 19:11:27.737][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-02-05 19:11:27.738][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-05 19:11:27.740][biodb::testContext]
biodb.INFO [2025-02-05 19:11:27.749][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-05 19:11:27.752][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-02-05 19:11:27.763][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-05 19:11:27.765][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-05 19:11:27.767][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-05 19:11:27.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:27.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:27.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:27.773][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-05 19:11:27.801][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-05 19:11:27.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:27.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:27.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:27.808][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-05 19:11:27.809][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-05 19:11:27.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:27.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:27.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:27.814][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-05 19:11:27.816][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-05 19:11:27.817][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-05 19:11:27.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:27.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:27.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:27.822][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-05 19:11:27.823][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-05 19:11:27.824][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-05 19:11:27.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:27.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:27.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:27.829][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-05 19:11:27.831][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-05 19:11:27.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:27.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:27.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:27.836][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-05 19:11:27.838][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-05 19:11:27.839][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-05 19:11:27.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:27.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:27.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:27.843][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-05 19:11:27.845][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-05 19:11:27.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:27.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:27.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:27.865][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-05 19:11:27.866][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-05 19:11:27.867][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-05 19:11:27.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:27.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:27.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:27.872][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-05 19:11:27.873][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-05 19:11:27.874][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-05 19:11:27.875][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-05 19:11:27.876][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-05 19:11:27.877][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-05 19:11:27.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:27.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:27.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:27.882][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-05 19:11:27.883][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-05 19:11:27.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:27.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:27.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:27.888][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-05 19:11:27.889][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-05 19:11:27.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:27.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:27.892][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[2025-02-05 19:11:27.893][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-05 19:11:27.895][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-05 19:11:27.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:27.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:27.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:27.899][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-05 19:11:27.901][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-05 19:11:27.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:27.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:27.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:27.904][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-05 19:11:27.906][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-05 19:11:27.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:27.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:27.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:27.910][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-05 19:11:27.911][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-05 19:11:27.935][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-05 19:11:27.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:27.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:27.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:27.941][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-05 19:11:27.942][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-05 19:11:27.944][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-05 19:11:27.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:27.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:27.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:27.951][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-05 19:11:27.996][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-05 19:11:28.016][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-05 19:11:28.017][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-05 19:11:28.019][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-05 19:11:28.020][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-05 19:11:28.021][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-05 19:11:28.022][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-05 19:11:28.023][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-05 19:11:28.024][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-05 19:11:28.025][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-05 19:11:28.027][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-05 19:11:28.028][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-05 19:11:28.029][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-05 19:11:28.030][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:11:28.031][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-05 19:11:28.032][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-05 19:11:28.032][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-05 19:11:28.032][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-05 19:11:28.032][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-05 19:11:28.032][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-05 19:11:28.034][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-05 19:11:28.034][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:11:28.036][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:11:28.037][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-05 19:11:28.038][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:11:28.039][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:11:28.040][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-05 19:11:28.041][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:11:28.042][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-05 19:11:28.043][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-05 19:11:28.045][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-05 19:11:28.046][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:11:28.047][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-05 19:11:28.050][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-05 19:11:28.051][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-05 19:11:28.052][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-05 19:11:28.054][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-05 19:11:28.055][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-05 19:11:28.056][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-05 19:11:28.058][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-05 19:11:28.059][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-05 19:11:28.060][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-05 19:11:28.062][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-05 19:11:28.063][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-05 19:11:28.064][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-05 19:11:28.065][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-05 19:11:28.067][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:11:28.068][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-05 19:11:28.069][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-05 19:11:28.069][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-05 19:11:28.069][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-05 19:11:28.069][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-05 19:11:28.069][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-05 19:11:28.070][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-05 19:11:28.072][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:11:28.073][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:11:28.074][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-05 19:11:28.076][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:11:28.077][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:11:28.078][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-05 19:11:28.080][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:11:28.081][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-05 19:11:28.082][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-05 19:11:28.083][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-05 19:11:28.085][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:11:28.086][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-05 19:11:28.089][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-05 19:11:28.090][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-05 19:11:28.092][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-05 19:11:28.093][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-05 19:11:28.094][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-05 19:11:28.095][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-05 19:11:28.097][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-05 19:11:28.098][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-05 19:11:28.099][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-05 19:11:28.101][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-05 19:11:28.102][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-05 19:11:28.103][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-05 19:11:28.104][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-05 19:11:28.105][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:11:28.107][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-05 19:11:28.108][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:11:28.110][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-05 19:11:28.111][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:11:28.112][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:11:28.113][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-05 19:11:28.115][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:11:28.116][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:11:28.117][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-05 19:11:28.118][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:11:28.120][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-05 19:11:28.121][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-05 19:11:28.122][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-05 19:11:28.123][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:11:28.125][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-05 19:11:28.127][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-05 19:11:28.128][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-05 19:11:28.130][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-05 19:11:28.131][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-05 19:11:28.132][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-05 19:11:28.133][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-05 19:11:28.135][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-05 19:11:28.136][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-05 19:11:28.137][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-05 19:11:28.139][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-05 19:11:28.140][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-05 19:11:28.141][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-05 19:11:28.143][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-05 19:11:28.144][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:11:28.146][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-05 19:11:28.147][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:11:28.148][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-05 19:11:28.149][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:11:28.157][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:11:28.159][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-05 19:11:28.161][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:11:28.162][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:11:28.163][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-05 19:11:28.164][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:11:28.165][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-05 19:11:28.167][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-05 19:11:28.168][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-05 19:11:28.169][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:11:28.174][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-05 19:11:28.175][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.181][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.DEBUG[2025-02-05 19:11:28.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.192][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.DEBUG[2025-02-05 19:11:28.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.252][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[2025-02-05 19:11:28.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.269][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[2025-02-05 19:11:28.271][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-05 19:11:28.277][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-05 19:11:28.279][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-05 19:11:28.281][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-05 19:11:28.283][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-05 19:11:28.285][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-05 19:11:28.287][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-05 19:11:28.289][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-05 19:11:28.291][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-05 19:11:28.293][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-05 19:11:28.295][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-05 19:11:28.297][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-05 19:11:28.299][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-05 19:11:28.301][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-05 19:11:28.303][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-05 19:11:28.305][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-05 19:11:28.307][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-05 19:11:28.309][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-05 19:11:28.311][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-05 19:11:28.313][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-05 19:11:28.315][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-05 19:11:28.317][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-05 19:11:28.318][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-05 19:11:28.320][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-05 19:11:28.322][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-05 19:11:28.324][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-05 19:11:28.326][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-05 19:11:28.328][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-05 19:11:28.330][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-05 19:11:28.331][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-05 19:11:28.333][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-05 19:11:28.334][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-05 19:11:28.336][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-05 19:11:28.338][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-05 19:11:28.339][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-05 19:11:28.341][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-05 19:11:28.343][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-05 19:11:28.344][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-05 19:11:28.346][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-05 19:11:28.348][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-05 19:11:28.349][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-05 19:11:28.351][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-05 19:11:28.353][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-05 19:11:28.355][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-05 19:11:28.359][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-05 19:11:28.362][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-05 19:11:28.363][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-05 19:11:28.366][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-05 19:11:28.368][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-05 19:11:28.370][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-05 19:11:28.372][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-05 19:11:28.374][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-05 19:11:28.376][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-05 19:11:28.378][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-05 19:11:28.381][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-05 19:11:28.383][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-05 19:11:28.385][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-05 19:11:28.387][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-05 19:11:28.389][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-05 19:11:28.391][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-05 19:11:28.393][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-05 19:11:28.396][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-05 19:11:28.398][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-05 19:11:28.400][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-05 19:11:28.402][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-05 19:11:28.404][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-05 19:11:28.406][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-05 19:11:28.408][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-05 19:11:28.410][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-05 19:11:28.412][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-05 19:11:28.413][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-05 19:11:28.416][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-05 19:11:28.417][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-05 19:11:28.419][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-05 19:11:28.421][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-05 19:11:28.422][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-05 19:11:28.423][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-05 19:11:28.425][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-05 19:11:28.426][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-05 19:11:28.428][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-05 19:11:28.430][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-05 19:11:28.432][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-05 19:11:28.441][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-05 19:11:28.447][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-05 19:11:28.449][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-05 19:11:28.454][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-05 19:11:28.455][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.457][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:28.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:28.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:28.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:28.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:28.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:28.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.486][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[2025-02-05 19:11:28.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:28.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:28.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.495][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.DEBUG[2025-02-05 19:11:28.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:28.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:28.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.502][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[2025-02-05 19:11:28.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:28.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:28.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.510][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.DEBUG[2025-02-05 19:11:28.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:28.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:28.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.517][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[2025-02-05 19:11:28.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:28.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:28.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:28.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:28.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:28.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:28.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.538][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[2025-02-05 19:11:28.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:28.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:28.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:28.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:28.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:28.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:28.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:28.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:28.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:28.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:28.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:28.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:28.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:11:28.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:28.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:28.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:28.590][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-02-05 19:11:28.601][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-02-05 19:11:28.604][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-05 19:11:28.606][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-05 19:11:28.607][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-05 19:11:28.608][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-05 19:11:28.609][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-05 19:11:28.610][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-05 19:11:28.612][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-05 19:11:28.613][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-02-05 19:11:28.614][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-05 19:11:28.615][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-05 19:11:28.616][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-05 19:11:28.617][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-02-05 19:11:28.618][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-05 19:11:28.619][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-02-05 19:11:28.619][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-02-05 19:11:28.619][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-02-05 19:11:28.619][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-02-05 19:11:28.619][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-02-05 19:11:28.619][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-02-05 19:11:28.619][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-02-05 19:11:28.619][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-02-05 19:11:28.619][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-02-05 19:11:28.619][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-02-05 19:11:28.619][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-02-05 19:11:28.620][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-05 19:11:28.622][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-05 19:11:28.622][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-05 19:11:28.622][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-05 19:11:28.623][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-05 19:11:28.624][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:11:28.625][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:11:28.626][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-05 19:11:28.627][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:11:28.628][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:11:28.629][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-05 19:11:28.630][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:11:28.630][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-02-05 19:11:28.631][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-05 19:11:28.632][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-05 19:11:28.633][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-05 19:11:28.634][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-02-05 19:11:28.634][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-02-05 19:11:28.641][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-05 19:11:28.643][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-05 19:11:28.645][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-02-05 19:11:28.646][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-05 19:11:28.648][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-05 19:11:28.650][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-05 19:11:28.682][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-02-05 19:11:28.684][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-02-05 19:11:28.689][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-02-05 19:11:28.693][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-02-05 19:11:28.708][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-05 19:11:28.709][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-05 19:11:28.711][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-02-05 19:11:28.712][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-02-05 19:11:28.724][biodb::testThat]
biodb.INFO [2025-02-05 19:11:28.726][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-02-05 19:11:28.727][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:11:28.728][biodb::testThat]
biodb.TRACE[2025-02-05 19:11:28.733][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-02-05 19:11:28.736][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:11:28.740][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:11:28.750][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:28.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:28.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:28.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:28.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:28.772][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:28.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:11:28.782][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:28.784][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:28.785][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.786][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:28.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:28.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.806][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:28.807][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:28.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.809][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.842][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:28.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:28.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.847][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:28.848][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:28.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.851][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.853][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:28.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:28.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.857][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:28.858][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:28.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.860][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.861][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:28.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:28.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.866][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:28.867][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:28.868][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.868][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.870][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:28.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:28.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.875][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:28.876][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:28.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.878][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.880][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:28.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:28.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.884][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:28.885][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:28.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.887][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.888][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:28.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:28.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.893][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:28.894][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:28.896][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.897][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:28.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:28.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.904][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:28.905][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:28.906][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.908][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.910][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:28.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:28.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.915][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:28.916][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:28.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.918][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.920][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:28.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:28.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.925][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:28.926][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:28.927][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.928][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.930][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:28.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:28.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:28.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:28.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.940][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:28.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:28.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:28.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:28.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:28.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:28.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:28.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:28.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:28.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:28.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:28.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:28.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:29.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:29.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:29.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:29.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:29.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:29.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:29.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:29.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:29.061][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-02-05 19:11:29.064][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:29.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:29.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.069][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:29.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:29.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.098][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:29.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:29.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.104][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:29.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:29.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:29.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:29.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.112][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:29.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:29.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.117][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-05 19:11:29.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-05 19:11:29.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.121][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-05 19:11:29.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-05 19:11:29.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.126][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-05 19:11:29.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-05 19:11:29.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.131][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-05 19:11:29.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-05 19:11:29.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:29.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:29.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:29.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:29.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:29.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:29.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:29.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:29.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:29.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:29.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:29.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:29.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:29.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:29.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:29.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:29.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:29.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:29.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:29.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:29.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:29.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:29.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:29.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:29.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:29.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:29.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:29.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:29.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.275][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:29.277][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:29.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.279][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:29.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:29.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:29.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:29.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:29.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:29.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:29.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:29.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.313][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:29.314][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:29.315][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.316][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:29.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:29.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.332][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:29.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:29.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.338][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:29.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:29.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.343][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:29.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:29.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.348][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:29.350][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:29.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.352][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.353][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:29.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:29.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.370][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:29.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:29.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.376][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:29.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:29.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.381][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:29.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:29.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.387][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:29.406][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:29.408][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.409][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.410][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:29.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:29.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:29.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:29.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:29.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:29.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:29.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:29.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.446][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:29.453][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:29.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.456][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.457][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:29.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:29.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:29.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:29.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:29.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:29.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:29.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:29.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.486][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:29.487][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:29.488][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.490][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.490][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:29.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:29.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.506][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:29.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:29.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.513][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:29.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:29.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.518][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:29.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:29.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.524][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:29.525][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:29.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.528][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.529][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:29.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:29.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.546][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-05 19:11:29.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:29.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.553][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-05 19:11:29.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:29.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.557][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-05 19:11:29.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:29.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.562][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-05 19:11:29.563][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:29.564][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.565][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.567][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-05 19:11:29.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:29.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.583][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:29.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:29.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.589][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:29.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:29.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.593][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:29.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:29.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.597][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:29.598][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:29.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.600][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.601][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:29.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:29.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.618][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:29.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:29.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.624][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:29.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:29.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.629][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:29.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:29.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.633][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:29.634][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:29.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.637][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.638][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:29.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:29.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.654][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:29.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:29.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.658][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:29.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:29.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.663][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:29.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:29.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.667][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:29.669][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:29.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.671][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.672][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:29.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:29.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.692][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:29.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:29.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.698][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:29.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:29.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.702][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:29.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:29.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.707][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:29.708][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:29.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.710][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.711][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:29.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:29.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.726][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:29.728][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:29.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.731][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.739][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:29.741][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:29.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.743][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.750][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:29.752][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:29.753][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.754][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.762][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:29.764][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:29.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.767][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.774][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:29.776][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:29.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.778][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.786][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:29.788][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:29.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.791][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.798][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:29.799][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:29.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.801][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.808][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:29.810][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:29.811][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.813][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.820][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-05 19:11:29.822][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:29.823][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.824][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.832][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:29.834][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:29.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.836][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.844][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:29.846][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:29.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.849][ef$get] fields variable is a list.
biodb.INFO [2025-02-05 19:11:29.862][biodb::testThat]
biodb.INFO [2025-02-05 19:11:29.863][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-02-05 19:11:29.865][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:11:29.866][biodb::testThat]
biodb.DEBUG[2025-02-05 19:11:29.887][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-02-05 19:11:29.896][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:11:29.902][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-02-05 19:11:29.904][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:11:29.906][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-02-05 19:11:29.908][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:11:29.946][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:11:29.947][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:11:29.949][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:29.950][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:29.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:29.959][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:29.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:29.962][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:29.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:11:29.966][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:29.968][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:29.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.971][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:29.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:29.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:29.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:29.998][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:30.000][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:30.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.003][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.004][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:30.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:30.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.009][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:30.011][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:30.012][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.013][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.015][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:30.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:30.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.019][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:30.020][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:30.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.022][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:30.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:30.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.028][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:30.029][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:30.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.032][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.033][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:30.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:30.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.038][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:30.040][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:30.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.042][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.044][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:30.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:30.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.049][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:30.050][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:30.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.052][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.053][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:30.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:30.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.059][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:30.060][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:30.061][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.063][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:30.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:30.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.069][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:30.071][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:30.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.073][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.075][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:30.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:30.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.079][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:30.081][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:30.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.083][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.084][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:30.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:30.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.089][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:30.090][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:30.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.092][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.093][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:30.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:30.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:30.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:30.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.103][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:30.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:30.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:30.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:30.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.114][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:30.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:30.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:30.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:30.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:30.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:30.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:30.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:30.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:30.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:30.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:30.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:30.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:30.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:30.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:30.152][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-02-05 19:11:30.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-02-05 19:11:30.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-02-05 19:11:30.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-02-05 19:11:30.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-02-05 19:11:30.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-02-05 19:11:30.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-02-05 19:11:30.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-05 19:11:30.184][biodb::testThat]
biodb.INFO [2025-02-05 19:11:30.185][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-02-05 19:11:30.186][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:11:30.188][biodb::testThat]
biodb.TRACE[2025-02-05 19:11:30.191][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:30.193][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:30.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.195][ef$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:30.197][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-02-05 19:11:30.234][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:30.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:30.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.240][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:30.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:30.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.245][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:30.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:30.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:30.254][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-02-05 19:11:30.259][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-02-05 19:11:30.284][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:11:30.304][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-02-05 19:11:30.305][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:11:30.307][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-02-05 19:11:30.335][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[2025-02-05 19:11:30.339][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:11:30.341][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-05 19:11:30.342][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:11:30.344][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-02-05 19:11:30.347][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-02-05 19:11:30.370][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:30.372][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:30.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.374][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.376][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:30.377][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:30.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.379][ef$get] fields variable is a list.
biodb.INFO [2025-02-05 19:11:30.385][biodb::testThat]
biodb.INFO [2025-02-05 19:11:30.387][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-02-05 19:11:30.388][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:11:30.389][biodb::testThat]
biodb.TRACE[2025-02-05 19:11:30.419][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:30.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:30.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.424][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:30.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:30.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.429][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:30.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:30.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:30.505][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[2025-02-05 19:11:30.509][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:11:30.511][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-05 19:11:30.512][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:11:30.514][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-02-05 19:11:30.556][biodb::testThat]
biodb.INFO [2025-02-05 19:11:30.557][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-02-05 19:11:30.559][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:11:30.560][biodb::testThat]
biodb.TRACE[2025-02-05 19:11:30.585][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:30.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:30.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.600][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:30.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:30.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.605][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:30.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:30.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.611][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:30.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:30.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.615][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:30.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:30.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:30.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:30.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.624][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-05 19:11:30.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-05 19:11:30.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.630][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-05 19:11:30.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-05 19:11:30.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.636][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-05 19:11:30.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-05 19:11:30.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.641][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-05 19:11:30.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-05 19:11:30.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.669][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:30.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:30.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.674][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:30.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:30.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.679][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:30.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:30.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.685][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:30.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:30.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.689][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:30.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:30.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:30.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:30.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.700][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-05 19:11:30.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-05 19:11:30.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.706][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-05 19:11:30.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-05 19:11:30.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.711][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-05 19:11:30.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-05 19:11:30.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:30.715][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-05 19:11:30.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-05 19:11:30.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:30.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-05 19:11:30.728][biodb::testThat]
biodb.INFO [2025-02-05 19:11:30.729][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-02-05 19:11:30.730][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:11:30.731][biodb::testThat]
biodb.INFO [2025-02-05 19:11:30.743][biodb::testThat]
biodb.INFO [2025-02-05 19:11:30.745][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-02-05 19:11:30.746][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:11:30.748][biodb::testThat]
biodb.INFO [2025-02-05 19:11:30.761][biodb::testThat]
biodb.INFO [2025-02-05 19:11:30.762][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-02-05 19:11:30.764][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:11:30.765][biodb::testThat]
biodb.DEBUG[2025-02-05 19:11:30.770][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-02-05 19:11:31.463][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-02-05 19:11:32.830][biodb::testThat]
biodb.INFO [2025-02-05 19:11:32.832][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-02-05 19:11:32.833][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:11:32.835][biodb::testThat]
biodb.DEBUG[2025-02-05 19:11:33.237][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[2025-02-05 19:11:33.636][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:33.637][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:33.639][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:33.640][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:33.642][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:33.643][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:33.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:33.646][ef$get] fields variable is a list.
biodb.INFO [2025-02-05 19:11:33.648][biodb::testThat]
biodb.INFO [2025-02-05 19:11:33.650][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-02-05 19:11:33.651][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:11:33.652][biodb::testThat]
biodb.TRACE[2025-02-05 19:11:33.671][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:33.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:33.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:33.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:33.677][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:33.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:33.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:33.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:33.682][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:33.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:33.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:33.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:33.812][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[2025-02-05 19:11:33.816][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:11:33.819][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-05 19:11:33.821][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:11:33.823][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-02-05 19:11:33.923][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[2025-02-05 19:11:33.928][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:11:33.930][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-05 19:11:33.932][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:11:33.934][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-02-05 19:11:33.955][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-05 19:11:33.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-05 19:11:33.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:33.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:33.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:33.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:33.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:33.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:33.974][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:33.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:33.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:33.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:33.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:33.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:33.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:33.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:33.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:33.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:33.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:33.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:33.990][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:33.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:33.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:33.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:34.004][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[2025-02-05 19:11:34.009][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:11:34.011][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-02-05 19:11:34.013][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:11:34.015][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-02-05 19:11:34.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:34.020][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:34.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:34.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:34.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:34.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:34.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:34.034][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-02-05 19:11:34.109][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:11:34.112][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-02-05 19:11:34.114][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:11:34.115][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:11:34.117][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:11:34.118][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:11:34.120][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:11:34.121][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:11:34.125][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:34.127][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:34.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:34.136][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:34.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:34.139][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:34.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:34.142][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-02-05 19:11:34.146][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:11:34.148][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:11:34.149][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-02-05 19:11:44.531][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-02-05 19:11:44.908][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:11:44.911][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-02-05 19:11:44.932][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-02-05 19:11:44.936][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-02-05 19:11:44.939][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:11:44.941][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:11:44.943][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:11:44.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:44.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:44.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:44.976][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:44.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:44.979][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:44.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:11:44.984][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:44.985][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:44.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:44.988][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:44.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:44.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:44.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:44.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:44.998][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:45.000][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:45.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.002][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.003][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:45.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:45.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.008][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:45.009][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:45.010][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.011][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.014][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:45.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:45.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.019][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:45.020][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:45.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.022][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.023][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:45.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:45.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.029][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:45.030][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:45.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.032][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.034][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:45.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:45.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.039][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:45.041][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:45.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.043][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.045][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:45.047][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:45.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.049][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.050][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:45.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:45.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.064][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:45.071][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:45.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.073][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:45.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:45.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.080][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:45.081][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:45.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.083][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.086][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:45.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:45.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.093][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:45.094][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:45.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.097][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.098][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:45.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:45.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.103][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:45.105][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:45.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.107][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.108][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:45.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:45.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.114][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:45.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:45.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:45.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:45.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:45.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:45.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.128][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:45.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:45.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:45.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:45.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:45.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:45.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:45.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:45.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:45.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:45.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:45.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:45.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:45.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:45.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:45.164][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-02-05 19:11:45.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:45.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:45.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.182][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:45.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:45.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:45.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:45.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:45.194][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[2025-02-05 19:11:45.199][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:11:45.201][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-02-05 19:11:45.202][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:11:45.204][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-02-05 19:11:45.223][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:45.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:45.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:45.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:45.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:45.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:45.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:11:45.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:45.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:45.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:45.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:45.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:45.257][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:45.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:45.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:45.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:45.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:45.264][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:45.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:45.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:45.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:45.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:45.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:45.278][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-02-05 19:11:45.280][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:11:45.282][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-02-05 19:11:45.284][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:11:45.285][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:11:45.286][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:11:45.288][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:11:45.289][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:11:45.291][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:11:45.308][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:45.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:45.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:45.319][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:45.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:45.322][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:45.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:45.325][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-02-05 19:11:45.347][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:11:45.349][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:11:45.370][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-02-05 19:11:45.736][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-02-05 19:11:46.102][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:11:46.105][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-02-05 19:11:46.110][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-02-05 19:11:46.115][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-02-05 19:11:46.117][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:11:46.119][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:11:46.121][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:11:46.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:46.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:46.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:46.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:46.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:46.148][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:46.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:11:46.153][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:46.154][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:46.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.157][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:46.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:46.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.163][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:46.165][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:46.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.167][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.169][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:46.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:46.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.173][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:46.174][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:46.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.176][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.178][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:46.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:46.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.184][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:46.186][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:46.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.188][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.190][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:46.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:46.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.195][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:46.197][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:46.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.199][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.201][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:46.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:46.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.206][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:46.207][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:46.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.209][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.211][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:46.212][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:46.213][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.214][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.215][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:46.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:46.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.220][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:46.221][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:46.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.224][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:46.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:46.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.231][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:46.232][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:46.233][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.234][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.236][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:46.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:46.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.242][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:46.243][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:46.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.245][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.247][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:46.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:46.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.253][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:46.254][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:46.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.257][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.258][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:46.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:46.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:46.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:46.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:46.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:46.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:46.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:46.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.276][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:46.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:46.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:46.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:46.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:46.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:46.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:46.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:46.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:46.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:46.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:46.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:46.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:46.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:46.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:46.316][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-02-05 19:11:46.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:46.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:46.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.324][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:46.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:46.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:46.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:46.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:46.359][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[2025-02-05 19:11:46.364][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:11:46.366][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-05 19:11:46.368][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:11:46.370][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-02-05 19:11:46.373][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:46.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:46.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:46.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:46.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:46.386][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:46.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:11:46.389][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:46.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:46.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:46.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:46.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:46.400][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:46.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:46.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:46.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:46.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:46.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:46.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:46.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:46.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:46.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:46.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:46.418][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-02-05 19:11:46.419][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:11:46.421][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-02-05 19:11:46.423][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:11:46.425][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:11:46.426][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:11:46.427][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:11:46.429][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:11:46.430][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:11:46.434][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:46.435][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:46.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:46.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:46.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:46.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:46.447][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[2025-02-05 19:11:46.449][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-02-05 19:11:46.452][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:11:46.454][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:11:46.456][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-02-05 19:11:46.830][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-02-05 19:11:47.199][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:11:47.202][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-02-05 19:11:47.207][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-02-05 19:11:47.211][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-02-05 19:11:47.213][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:11:47.215][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:11:47.216][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:11:47.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:47.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:47.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:47.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:47.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:47.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:47.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:11:47.248][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:47.250][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:47.251][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.253][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:47.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:47.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.259][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:47.261][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:47.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.263][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.264][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:47.266][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:47.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.268][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.270][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:47.271][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:47.272][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.273][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.275][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:47.276][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:47.277][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.279][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.280][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:47.282][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:47.283][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.284][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.286][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:47.287][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:47.288][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.289][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.291][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:47.293][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:47.294][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.295][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.296][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:47.297][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:47.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.300][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.302][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:47.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:47.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.306][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:47.308][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:47.309][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.310][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.312][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:47.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:47.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.317][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:47.318][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:47.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.321][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.323][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:47.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:47.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:47.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:47.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:47.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:47.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:47.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:47.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:47.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:47.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:47.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:47.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:47.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:47.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:47.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:47.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:47.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:47.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:47.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:47.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:47.370][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-02-05 19:11:47.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:47.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:47.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:47.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:47.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:47.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:47.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.384][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:47.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:47.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:47.389][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:47.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:47.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:47.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:47.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:47.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:47.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:47.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:47.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:47.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:47.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:47.415][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-02-05 19:11:47.417][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:11:47.419][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-02-05 19:11:47.420][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:11:47.421][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:11:47.423][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:11:47.424][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:11:47.425][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:11:47.426][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:11:47.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:47.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:47.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:47.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:47.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:47.442][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:47.443][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[2025-02-05 19:11:47.445][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-02-05 19:11:47.448][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:11:47.449][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:11:47.451][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-02-05 19:11:47.843][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-02-05 19:11:48.206][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:11:48.209][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-02-05 19:11:48.214][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-02-05 19:11:48.217][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-02-05 19:11:48.219][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:11:48.220][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:11:48.221][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:11:48.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:48.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:48.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:48.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:48.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:48.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:48.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:11:48.239][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:48.240][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:48.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.243][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:48.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:48.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.249][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:48.250][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:48.251][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.252][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.254][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:48.254][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:48.256][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.257][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.259][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:48.260][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:48.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.262][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.263][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:48.264][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:48.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.266][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.268][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:48.269][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:48.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.271][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.272][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:48.274][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:48.275][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.275][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.277][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:48.278][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:48.279][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.280][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.281][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:48.283][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:48.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.285][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.287][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:48.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:48.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.291][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:48.292][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:48.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.294][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.295][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:48.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:48.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.300][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:48.301][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:48.302][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.303][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:48.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:48.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:48.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:48.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:48.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:48.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:48.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:48.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:48.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:48.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:48.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:48.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:48.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:48.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:48.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:48.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:48.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:48.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:48.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:48.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:48.362][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-02-05 19:11:48.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:48.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:48.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:48.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:48.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:48.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:48.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.378][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:48.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:48.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:48.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:48.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:48.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:48.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:48.388][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:48.389][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:48.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:48.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:48.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:48.398][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:48.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:48.401][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-02-05 19:11:48.402][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:11:48.404][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-02-05 19:11:48.406][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:11:48.407][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:11:48.408][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:11:48.410][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:11:48.411][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:11:48.412][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:11:48.416][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:48.417][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:48.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:48.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:48.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:48.429][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:48.430][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[2025-02-05 19:11:48.431][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-02-05 19:11:48.435][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:11:48.437][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:11:48.439][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-02-05 19:11:48.821][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-02-05 19:11:49.183][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:11:49.186][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-02-05 19:11:49.190][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-02-05 19:11:49.194][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-02-05 19:11:49.196][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:11:49.198][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:11:49.199][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:11:49.202][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:49.203][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:49.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:49.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:49.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:49.214][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:49.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:11:49.217][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:49.219][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:49.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.232][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:49.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:49.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.254][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:49.255][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:49.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.258][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.259][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:49.261][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:49.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.264][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.266][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:49.268][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:49.271][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.272][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.274][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:49.276][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:49.277][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.278][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.280][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:49.281][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:49.282][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.284][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.285][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:49.287][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:49.288][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.289][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.291][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:49.292][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:49.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.294][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.295][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:49.296][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:49.298][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.299][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.301][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:49.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:49.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.307][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:49.308][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:49.309][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.310][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.311][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:49.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:49.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.316][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:49.317][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:49.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.320][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.322][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:49.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:49.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:49.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:49.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:49.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:49.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.335][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:49.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:49.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:49.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:49.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:49.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:49.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:49.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:49.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:49.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:49.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:49.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:49.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:49.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:49.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:49.394][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-02-05 19:11:49.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:49.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:49.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.406][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:49.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:49.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.411][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:49.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:49.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.416][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:49.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:49.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:49.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:49.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:49.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:49.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:49.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:49.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:49.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:49.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:49.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:49.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:49.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:49.445][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-02-05 19:11:49.446][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:11:49.448][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-02-05 19:11:49.450][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:11:49.451][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:11:49.453][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:11:49.454][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:11:49.456][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:11:49.457][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:11:49.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:49.462][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:49.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:49.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:49.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:49.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:49.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:49.477][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-02-05 19:11:49.481][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:11:49.483][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:11:49.484][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-02-05 19:11:49.867][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-02-05 19:11:50.257][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:11:50.272][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-02-05 19:11:50.277][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-02-05 19:11:50.281][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-02-05 19:11:50.284][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:11:50.286][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:11:50.287][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:11:50.291][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:50.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:50.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:50.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:50.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:50.304][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:50.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:11:50.309][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:50.310][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:50.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.312][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:50.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:50.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.319][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:50.320][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:50.321][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.322][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.324][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:50.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:50.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.329][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:50.331][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:50.332][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.333][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.336][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:50.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:50.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.340][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:50.341][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:50.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.344][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.345][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:50.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:50.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.350][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:50.351][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:50.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.353][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.355][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:50.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:50.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.360][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:50.361][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:50.362][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.363][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.365][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:50.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:50.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.391][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:50.393][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:50.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.396][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.397][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:50.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:50.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.403][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:50.405][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:50.410][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.413][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:50.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:50.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.420][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:50.422][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:50.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.458][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:50.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:50.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.464][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:50.465][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:50.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.467][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.468][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:50.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:50.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.472][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:50.473][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:50.474][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.475][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.477][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:50.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:50.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:50.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:50.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:50.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:50.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:50.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:50.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:50.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:50.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:50.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:50.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:50.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:50.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:50.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:50.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:50.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:50.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:50.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:50.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:50.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:50.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:50.533][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-02-05 19:11:50.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:50.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:50.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:50.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:50.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:50.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:50.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:50.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:50.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:50.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:50.550][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:50.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:50.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:50.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:50.560][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:50.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:50.562][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-02-05 19:11:50.563][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:11:50.566][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-02-05 19:11:50.567][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:11:50.568][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:11:50.569][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:11:50.570][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:11:50.572][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:11:50.573][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:11:50.576][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:50.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:50.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:50.591][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:50.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:50.627][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:50.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:50.639][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-02-05 19:11:50.643][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:11:50.644][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:11:50.647][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-02-05 19:11:51.048][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-02-05 19:11:51.414][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:11:51.417][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-02-05 19:11:51.421][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-02-05 19:11:51.425][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-02-05 19:11:51.428][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:11:51.429][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:11:51.431][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:11:51.444][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:51.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:51.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:51.455][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:51.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:51.457][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:51.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:11:51.461][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:51.463][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:51.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.465][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:51.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:51.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.473][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:51.474][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:51.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.477][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.478][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:51.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:51.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.483][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:51.484][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:51.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.485][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.487][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:51.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:51.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.493][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:51.494][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:51.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.497][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.498][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:51.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:51.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.501][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:51.502][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:51.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.504][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.505][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:51.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:51.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.510][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:51.511][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:51.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.514][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.515][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:51.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:51.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.520][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:51.521][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:51.521][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.522][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.523][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:51.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:51.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.528][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:51.529][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:51.530][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.532][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.533][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:51.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:51.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.537][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:51.538][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:51.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.541][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.542][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:51.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:51.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.545][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:51.546][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:51.547][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.548][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.549][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:51.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:51.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.555][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:51.556][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:51.557][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.558][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.559][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:51.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:51.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:51.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:51.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:51.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:51.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:51.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:51.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:51.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:51.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:51.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:51.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:51.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:51.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:51.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:51.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:51.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:51.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:51.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:51.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:51.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:51.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:51.616][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-02-05 19:11:51.617][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:51.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:51.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:51.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:51.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:51.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:51.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:51.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:51.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:51.632][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:51.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:51.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:51.640][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:51.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:51.643][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:51.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:51.645][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-02-05 19:11:51.646][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:11:51.648][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-02-05 19:11:51.650][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:11:51.651][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:11:51.652][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:11:51.654][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:11:51.655][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:11:51.656][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:11:51.660][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:51.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:51.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:51.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:51.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:51.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:51.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:51.676][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-02-05 19:11:51.679][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:11:51.680][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:11:51.682][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-02-05 19:11:52.058][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-02-05 19:11:52.428][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:11:52.431][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-02-05 19:11:52.436][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-02-05 19:11:52.439][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-02-05 19:11:52.441][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:11:52.443][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:11:52.445][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:11:52.447][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:52.449][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:52.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:52.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:52.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:52.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:52.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:11:52.463][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:52.464][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:52.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.467][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:52.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:52.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.472][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:52.473][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:52.474][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.475][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.476][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:52.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:52.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.481][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:52.483][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:52.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.484][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.486][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:52.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:52.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.490][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:52.491][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:52.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.493][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:52.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:52.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.499][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:52.501][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:52.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.515][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.517][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:52.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:52.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.521][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:52.522][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:52.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.524][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.526][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:52.527][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:52.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.529][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.531][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:52.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:52.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.535][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:52.537][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:52.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.539][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:52.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:52.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.546][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:52.547][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:52.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.548][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.550][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:52.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:52.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.554][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:52.555][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:52.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.556][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.558][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:52.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:52.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.561][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:52.562][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:52.563][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.564][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.566][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:52.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:52.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.572][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:52.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:52.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:52.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:52.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:52.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:52.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:52.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:52.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:52.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:52.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:52.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:52.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:52.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:52.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:52.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:52.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:52.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:52.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:52.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:52.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:52.616][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-02-05 19:11:52.618][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:52.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:52.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.623][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:52.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:52.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:52.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:52.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:52.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:52.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:52.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:52.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:52.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:52.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:52.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:52.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:52.645][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[2025-02-05 19:11:52.646][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-02-05 19:11:52.647][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:11:52.649][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-02-05 19:11:52.650][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:11:52.651][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:11:52.652][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:11:52.654][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:11:52.655][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:11:52.656][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:11:52.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:52.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:52.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:52.676][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:52.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:52.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:52.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:52.681][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-02-05 19:11:52.685][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:11:52.685][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:11:52.687][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-02-05 19:11:53.058][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-02-05 19:11:53.433][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:11:53.436][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-02-05 19:11:53.441][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-02-05 19:11:53.445][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-02-05 19:11:53.448][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:11:53.450][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:11:53.451][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:11:53.454][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:53.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:53.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:53.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:53.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:53.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:53.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:11:53.472][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:53.474][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:53.474][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.475][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:53.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:53.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.481][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:53.483][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:53.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.485][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.486][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:53.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:53.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.492][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:53.493][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:53.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.496][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.498][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:53.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:53.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.504][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:53.505][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:53.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.507][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.508][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:53.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:53.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.513][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:53.514][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:53.515][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.517][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.518][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:53.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:53.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.523][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:53.524][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:53.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.526][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.527][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:53.528][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:53.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.530][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.532][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:53.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:53.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.537][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:53.539][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:53.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.541][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:53.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:53.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.546][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:53.548][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:53.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.550][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.552][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:53.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:53.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.556][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:53.558][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:53.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.561][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.562][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:53.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:53.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.568][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:53.569][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:53.570][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.571][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.572][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:53.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:53.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:53.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:53.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:53.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:53.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:53.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:53.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:53.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:53.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:53.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:53.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:53.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:53.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:53.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:53.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:53.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:53.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:53.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:53.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:53.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:53.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:53.636][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-02-05 19:11:53.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:53.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:53.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:53.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:53.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:53.646][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:53.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:53.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:53.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:53.651][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:53.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:53.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:53.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:53.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:53.662][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:53.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:53.664][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-02-05 19:11:53.665][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:11:53.667][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-02-05 19:11:53.669][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:11:53.670][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:11:53.671][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:11:53.673][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:11:53.674][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:11:53.674][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:11:53.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:53.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:53.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:53.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:53.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:53.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:53.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:53.693][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-02-05 19:11:53.696][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:11:53.697][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:11:53.699][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-02-05 19:11:54.069][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-02-05 19:11:54.431][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:11:54.433][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-02-05 19:11:54.437][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-02-05 19:11:54.441][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-02-05 19:11:54.443][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:11:54.445][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:11:54.446][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:11:54.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:54.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:54.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:54.458][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:54.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:54.460][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:54.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:11:54.464][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:54.466][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:54.467][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.469][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:54.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:54.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.484][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:54.486][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:54.487][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.489][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.490][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:54.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:54.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.496][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:54.498][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:54.500][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.501][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.503][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:54.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:54.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.509][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:54.510][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:54.511][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.512][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.514][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:54.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:54.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.519][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:54.520][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:54.521][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.522][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.524][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:54.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:54.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.528][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:54.530][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:54.531][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.532][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.534][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:54.535][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:54.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.537][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.539][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:54.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:54.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.543][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:54.544][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:54.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.546][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:54.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:54.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.553][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:54.554][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:54.555][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.556][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.558][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:54.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:54.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.563][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:54.564][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:54.566][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.567][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.568][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:54.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:54.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.573][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:54.575][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:54.576][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.577][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.579][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:54.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:54.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:54.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:54.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:54.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:54.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:54.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:54.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:54.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:54.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:54.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:54.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:54.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:54.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:54.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:54.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:54.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:54.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:54.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:54.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:54.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:54.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:54.633][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-02-05 19:11:54.634][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:54.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:54.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.638][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:54.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:54.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:54.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:54.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:54.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:54.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:54.653][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:54.654][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:54.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:54.661][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:54.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:54.664][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:54.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:54.666][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-02-05 19:11:54.667][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:11:54.670][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-02-05 19:11:54.671][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:11:54.672][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:11:54.674][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:11:54.676][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:11:54.677][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:11:54.678][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:11:54.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:54.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:54.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:54.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:54.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:54.695][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:54.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:54.697][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-02-05 19:11:54.701][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:11:54.703][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:11:54.704][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-02-05 19:11:55.088][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-02-05 19:11:55.457][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:11:55.460][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-02-05 19:11:55.465][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-02-05 19:11:55.470][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-02-05 19:11:55.471][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:11:55.473][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:11:55.474][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:11:55.477][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:55.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:55.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:55.485][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:55.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:55.487][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:55.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:11:55.492][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:55.494][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:55.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.496][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:55.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:55.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.501][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:55.502][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:55.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.504][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.505][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:55.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:55.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.509][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:55.510][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:55.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.513][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.514][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:55.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:55.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.519][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:55.520][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:55.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.523][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.524][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:55.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:55.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.528][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:55.529][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:55.530][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.531][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.532][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:55.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:55.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.537][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:55.538][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:55.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.540][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.542][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:55.543][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:55.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.545][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.547][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:55.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:55.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.551][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:55.553][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:55.554][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.555][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.568][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:55.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:55.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.574][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:55.575][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:55.576][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.577][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.579][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:55.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:55.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.583][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:55.584][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:55.586][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.587][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.588][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:55.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:55.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.592][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:55.594][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:55.595][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.596][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.597][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:55.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:55.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:55.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:55.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:55.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:55.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:55.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:55.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:55.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:55.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:55.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:55.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:55.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:55.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:55.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:55.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:55.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:55.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:55.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:55.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:55.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:55.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:55.645][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-02-05 19:11:55.646][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:55.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:55.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.651][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:55.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:55.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:55.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:55.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:55.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:55.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:55.660][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:55.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:55.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:55.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:55.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:55.671][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:55.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:55.674][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-02-05 19:11:55.676][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:11:55.677][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-02-05 19:11:55.679][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:11:55.680][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:11:55.681][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:11:55.682][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:11:55.683][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:11:55.685][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:11:55.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:55.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:55.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:55.698][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:55.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:55.700][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:55.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:55.702][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-02-05 19:11:55.706][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:11:55.707][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:11:55.709][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-02-05 19:11:56.080][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-02-05 19:11:56.445][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:11:56.448][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-02-05 19:11:56.465][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-02-05 19:11:56.468][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-02-05 19:11:56.470][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:11:56.471][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:11:56.472][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:11:56.474][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:56.475][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:56.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:56.483][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:56.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:56.486][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:56.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:11:56.490][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:56.492][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:56.493][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.494][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:56.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:56.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.501][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:56.502][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:56.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.504][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.506][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:56.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:56.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.511][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:56.513][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:56.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.514][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.515][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:56.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:56.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.520][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:56.522][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:56.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.524][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.525][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:56.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:56.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.531][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:56.532][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:56.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.535][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.536][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:56.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:56.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.541][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:56.542][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:56.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.544][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.545][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:56.546][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:56.547][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.549][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.550][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:56.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:56.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.555][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:56.556][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:56.558][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.559][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:56.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:56.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.565][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:56.567][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:56.568][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.569][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.571][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:56.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:56.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.577][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:56.578][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:56.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.580][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.581][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:56.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:56.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.584][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:56.585][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:56.586][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.587][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.588][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:56.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:56.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:56.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:56.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:56.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:56.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:56.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:56.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:56.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:56.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:56.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:56.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:56.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:56.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:56.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:56.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:56.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:56.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:56.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:56.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:56.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:56.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:56.635][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-02-05 19:11:56.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:56.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:56.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:56.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:56.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:56.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:56.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:56.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:56.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:56.648][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:56.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:56.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:56.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:56.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:56.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:56.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:56.661][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-02-05 19:11:56.662][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:11:56.664][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-02-05 19:11:56.666][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:11:56.668][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:11:56.669][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:11:56.670][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:11:56.671][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:11:56.672][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:11:56.675][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:56.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:56.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:56.683][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:56.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:56.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:56.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:56.689][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-02-05 19:11:56.692][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:11:56.693][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:11:56.695][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-02-05 19:11:57.056][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-02-05 19:11:57.422][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:11:57.424][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-02-05 19:11:57.429][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-02-05 19:11:57.433][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-02-05 19:11:57.435][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:11:57.437][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:11:57.438][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:11:57.440][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:57.441][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:57.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:57.450][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:57.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:57.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:57.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:11:57.456][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:57.457][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:57.458][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.459][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:57.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:57.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.465][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:57.466][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:57.467][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.468][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.469][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:57.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:57.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.474][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:57.475][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:57.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.476][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.478][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:57.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:57.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.483][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:57.485][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:57.486][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.499][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.501][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:57.503][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:57.505][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.506][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.508][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:57.509][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:57.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.511][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.512][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:57.513][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:57.515][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.515][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.517][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:57.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:57.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.522][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:57.523][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:57.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.525][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:57.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:57.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.530][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:57.531][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:57.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.533][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.534][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:57.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:57.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.538][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:57.539][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:57.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.541][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.543][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:57.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:57.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.548][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:57.550][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:57.551][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.552][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:57.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:57.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:57.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:57.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:57.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:57.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:57.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:57.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:57.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:57.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:57.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:57.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:57.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:57.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:57.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:57.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:57.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:57.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:57.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:57.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:57.601][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-02-05 19:11:57.602][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:57.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:57.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.608][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:57.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:57.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:57.612][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:57.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:57.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:57.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:57.617][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:57.618][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:57.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:57.627][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:57.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:57.630][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:57.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:57.633][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-02-05 19:11:57.634][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:11:57.636][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-02-05 19:11:57.638][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:11:57.639][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:11:57.641][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:11:57.642][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:11:57.644][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:11:57.645][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:11:57.648][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:57.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:57.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:57.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:57.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:57.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:57.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:57.671][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-02-05 19:11:57.674][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:11:57.676][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:11:57.677][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-02-05 19:11:58.040][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-02-05 19:11:58.399][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:11:58.402][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-02-05 19:11:58.407][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-02-05 19:11:58.410][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-02-05 19:11:58.413][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:11:58.414][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:11:58.416][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:11:58.418][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:58.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:58.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:58.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:58.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:58.428][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:58.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:11:58.432][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:58.433][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:58.434][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.435][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:58.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:58.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.441][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:58.442][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:58.443][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.444][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.446][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:58.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:58.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.450][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:58.451][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:58.452][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.453][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.455][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:58.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:58.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.459][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:58.460][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:58.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.462][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.463][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:58.464][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:58.465][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.466][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.467][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:58.468][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:58.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.469][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.470][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:58.471][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:58.473][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.474][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.475][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:58.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:58.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.480][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:58.481][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:58.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.482][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:58.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:58.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.487][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:58.489][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:58.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.491][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.493][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:58.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:58.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.498][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:58.499][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:58.500][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.501][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.502][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:58.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:58.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.506][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:58.507][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:58.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.510][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.511][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:58.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:58.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:58.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:58.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:58.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:58.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:58.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:58.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:58.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:58.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:58.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:58.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:58.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:58.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:58.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:58.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:58.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:58.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:58.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:58.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:58.559][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-02-05 19:11:58.560][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:58.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:58.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:58.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:58.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:58.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:58.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:58.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:58.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:58.571][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:58.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:58.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:58.579][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:58.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:58.580][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:58.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:58.583][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-02-05 19:11:58.584][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:11:58.585][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-02-05 19:11:58.587][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:11:58.588][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:11:58.589][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:11:58.590][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:11:58.592][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:11:58.593][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:11:58.596][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:58.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:58.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:58.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:58.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:58.606][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:58.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:58.609][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-02-05 19:11:58.612][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:11:58.614][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:11:58.615][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-02-05 19:11:58.984][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-02-05 19:11:59.353][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:11:59.355][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-02-05 19:11:59.360][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-02-05 19:11:59.363][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-02-05 19:11:59.365][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:11:59.366][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:11:59.367][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:11:59.369][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:59.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:59.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:59.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:59.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:59.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:59.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:11:59.384][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:59.385][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:59.386][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.387][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:59.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:59.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.393][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:59.394][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:59.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.396][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.397][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:11:59.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:11:59.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.402][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:59.403][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:59.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.406][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.417][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:11:59.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:11:59.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.422][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:59.423][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:59.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.425][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.426][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:11:59.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:11:59.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.430][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:59.431][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:59.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.433][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.434][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:11:59.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:11:59.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.439][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:59.440][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:11:59.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.442][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.443][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:59.445][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:59.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.446][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.448][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:11:59.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:59.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.452][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:59.453][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:59.454][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.455][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:59.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:11:59.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.460][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:59.461][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:59.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.464][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.465][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:11:59.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:11:59.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.470][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:59.471][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:59.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.473][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.475][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:11:59.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:11:59.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.480][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:59.481][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:59.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.483][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.484][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:11:59.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:11:59.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:59.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:59.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:59.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:59.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:59.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:59.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.501][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:11:59.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:11:59.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:59.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:59.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:59.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:59.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:59.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:59.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:59.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:59.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:59.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:59.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:11:59.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:11:59.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:59.530][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-02-05 19:11:59.531][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:59.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:59.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:59.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:59.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:11:59.538][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:59.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:11:59.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:11:59.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:11:59.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:59.542][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:59.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:59.556][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:59.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:59.558][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:59.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:59.560][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-02-05 19:11:59.561][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:11:59.563][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-02-05 19:11:59.564][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:11:59.566][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:11:59.567][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:11:59.568][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:11:59.570][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:11:59.571][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:11:59.574][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:11:59.575][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:11:59.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:11:59.583][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:11:59.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:11:59.585][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:11:59.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:11:59.588][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-02-05 19:11:59.592][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:11:59.594][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:11:59.595][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-02-05 19:11:59.967][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-02-05 19:12:00.331][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2025-02-05 19:12:00.332][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-02-05 19:12:00.334][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-02-05 19:12:00.338][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-02-05 19:12:00.341][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-02-05 19:12:00.343][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:12:00.345][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:12:00.346][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:12:00.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:00.348][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:00.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:00.356][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:00.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:00.358][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:00.359][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[2025-02-05 19:12:00.362][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:00.362][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:00.363][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.365][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:00.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:00.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.370][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:00.371][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:00.372][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.374][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.375][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:00.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:00.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.380][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:00.381][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:00.381][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.382][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.384][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:00.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:00.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.389][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:00.390][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:00.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.393][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.394][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:00.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:00.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.399][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:00.400][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:00.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.403][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.404][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:00.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:00.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.409][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:00.410][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:00.411][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.412][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.414][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:00.415][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:00.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.418][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.419][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:00.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:00.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.424][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:00.425][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:00.426][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.427][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:00.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:00.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.434][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:00.434][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:00.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.436][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.449][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:00.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:00.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.454][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:00.456][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:00.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.458][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.459][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:00.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:00.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.462][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:00.464][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:00.465][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.465][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.466][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:00.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:00.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:00.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:00.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:00.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:00.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:00.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:00.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:00.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:00.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:00.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:00.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:00.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:00.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:00.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:00.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:00.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:00.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:00.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:00.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:00.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:00.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:00.510][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-02-05 19:12:00.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:00.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:00.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:00.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:00.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:00.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:00.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:00.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:00.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:00.526][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:00.527][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:00.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:00.535][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:00.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:00.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:00.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:00.541][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-02-05 19:12:00.542][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:12:00.545][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-02-05 19:12:00.546][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:12:00.548][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:12:00.549][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:12:00.551][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:12:00.552][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:12:00.554][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:12:00.557][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:00.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:00.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:00.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:00.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:00.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:00.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:00.573][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-02-05 19:12:00.576][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:00.578][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:00.580][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-02-05 19:12:00.954][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-02-05 19:12:01.362][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:01.364][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-02-05 19:12:01.368][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-02-05 19:12:01.372][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-02-05 19:12:01.374][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:12:01.376][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:12:01.387][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:12:01.389][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:01.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:01.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:01.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:01.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:01.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:01.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:01.407][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:01.408][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:01.409][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.410][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:01.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:01.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.415][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:01.416][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:01.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.417][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.419][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:01.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:01.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.422][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:01.423][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:01.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.425][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.426][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:01.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:01.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.430][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:01.431][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:01.431][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.432][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.433][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:01.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:01.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.437][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:01.438][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:01.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.439][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.440][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:01.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:01.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.444][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:01.445][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:01.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.446][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.448][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:01.448][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:01.449][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.450][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.451][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:01.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:01.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.455][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:01.456][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:01.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.457][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:01.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:01.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.462][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:01.463][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:01.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.465][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:01.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:01.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.469][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:01.470][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:01.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.472][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.473][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:01.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:01.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.478][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:01.479][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:01.480][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.481][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.482][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:01.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:01.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:01.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:01.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:01.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:01.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:01.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:01.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:01.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:01.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:01.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:01.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:01.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:01.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:01.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:01.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:01.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:01.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:01.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:01.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:01.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:01.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:01.534][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-02-05 19:12:01.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:01.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:01.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:01.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:01.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:01.544][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:01.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:01.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:01.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:01.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:01.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:01.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:01.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:01.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:01.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:01.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:01.559][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-02-05 19:12:01.560][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:12:01.561][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-02-05 19:12:01.563][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:12:01.564][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:12:01.565][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:12:01.566][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:12:01.567][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:12:01.568][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:12:01.570][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:01.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:01.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:01.579][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:01.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:01.582][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:01.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:01.584][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-02-05 19:12:01.586][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:01.588][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:01.589][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-02-05 19:12:01.957][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-02-05 19:12:02.330][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:02.334][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-02-05 19:12:02.339][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-02-05 19:12:02.343][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-02-05 19:12:02.345][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:12:02.347][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:12:02.348][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:12:02.350][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:02.351][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:02.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:02.359][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:02.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:02.362][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:02.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:02.367][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:02.368][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:02.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.370][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:02.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:02.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.376][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:02.377][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:02.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.379][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.381][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:02.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:02.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.385][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:02.386][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:02.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.388][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.390][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:02.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:02.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.394][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:02.395][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:02.396][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.397][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.398][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:02.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:02.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.413][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:02.415][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:02.416][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.417][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.418][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:02.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:02.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.422][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:02.423][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:02.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.425][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.426][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:02.427][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:02.429][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.429][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.431][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:02.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:02.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.435][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:02.437][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:02.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.439][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:02.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:02.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.446][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:02.447][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:02.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.449][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.450][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:02.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:02.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.455][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:02.456][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:02.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.458][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.460][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:02.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:02.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.465][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:02.466][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:02.467][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.468][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.470][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:02.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:02.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:02.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:02.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:02.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:02.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:02.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:02.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:02.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:02.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:02.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:02.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:02.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:02.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:02.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:02.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:02.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:02.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:02.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:02.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:02.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:02.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:02.518][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-02-05 19:12:02.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:02.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:02.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.524][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:02.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:02.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:02.528][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:02.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:02.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:02.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:02.532][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:02.533][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:02.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:02.541][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:02.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:02.543][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:02.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:02.546][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-02-05 19:12:02.548][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:12:02.550][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-02-05 19:12:02.551][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:12:02.553][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:12:02.561][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:12:02.562][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:12:02.563][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:12:02.564][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:12:02.567][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:02.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:02.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:02.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:02.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:02.579][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:02.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:02.582][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.INFO [2025-02-05 19:12:02.586][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2025-02-05 19:12:02.588][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:02.589][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:02.590][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-02-05 19:12:02.979][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-02-05 19:12:03.348][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:03.351][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-02-05 19:12:03.357][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-02-05 19:12:03.361][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-02-05 19:12:03.364][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:12:03.365][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:12:03.367][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:12:03.370][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:03.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:03.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:03.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:03.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:03.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:03.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:03.387][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:03.388][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:03.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.391][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:03.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:03.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.397][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:03.399][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:03.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.401][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.403][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:03.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:03.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.408][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:03.409][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:03.411][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.412][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.414][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:03.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:03.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.419][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:03.421][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:03.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.423][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.425][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:03.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:03.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.430][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:03.431][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:03.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.433][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.435][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:03.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:03.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.440][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:03.441][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:03.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.444][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.445][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:03.447][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:03.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.449][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.451][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:03.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:03.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.456][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:03.458][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:03.459][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.460][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:03.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:03.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.467][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:03.468][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:03.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.471][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.473][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:03.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:03.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.479][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:03.481][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:03.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.483][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.494][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:03.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:03.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.506][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:03.508][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:03.509][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.511][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.513][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:03.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:03.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:03.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:03.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:03.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:03.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:03.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:03.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:03.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:03.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:03.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:03.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:03.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:03.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:03.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:03.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:03.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:03.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:03.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:03.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:03.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:03.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:03.573][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-02-05 19:12:03.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:03.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:03.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.579][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:03.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:03.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:03.584][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:03.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:03.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:03.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:03.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:03.591][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:03.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:03.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:03.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:03.600][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:03.602][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.DEBUG[2025-02-05 19:12:03.603][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-02-05 19:12:03.604][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:12:03.607][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-02-05 19:12:03.608][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:12:03.610][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:12:03.611][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:12:03.613][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:12:03.614][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:12:03.615][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:12:03.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:03.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:03.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:03.629][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:03.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:03.631][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:03.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:03.634][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-02-05 19:12:03.638][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:03.639][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:03.641][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-02-05 19:12:04.019][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-02-05 19:12:04.381][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:04.385][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-02-05 19:12:04.390][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-02-05 19:12:04.394][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-02-05 19:12:04.397][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:12:04.399][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:12:04.401][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:12:04.403][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:04.404][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:04.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:04.414][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:04.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:04.430][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:04.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:04.436][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:04.438][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:04.439][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.441][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:04.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:04.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.448][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:04.449][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:04.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.452][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.474][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:04.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:04.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.481][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:04.483][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:04.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.486][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.488][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:04.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:04.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.494][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:04.495][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:04.497][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.498][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.500][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:04.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:04.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.505][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:04.507][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:04.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.509][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.511][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:04.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:04.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.517][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:04.518][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:04.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.521][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.522][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:04.524][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:04.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.526][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.528][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:04.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:04.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.534][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:04.535][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:04.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.538][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:04.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:04.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.544][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:04.546][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:04.547][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.548][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.550][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:04.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:04.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.555][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:04.557][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:04.558][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.559][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.560][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:04.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:04.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.566][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:04.567][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:04.568][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.570][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.571][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:04.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:04.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:04.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:04.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:04.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:04.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:04.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:04.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:04.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:04.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:04.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:04.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:04.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:04.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:04.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:04.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:04.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:04.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:04.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:04.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:04.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:04.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:04.648][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-02-05 19:12:04.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:04.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:04.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.654][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:04.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:04.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:04.659][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:04.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:04.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:04.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:04.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:04.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:04.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:04.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:04.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:04.677][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:04.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:04.680][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-02-05 19:12:04.682][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:12:04.684][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-02-05 19:12:04.686][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:12:04.687][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:12:04.689][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:12:04.690][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:12:04.691][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:12:04.693][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:12:04.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:04.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:04.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:04.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:04.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:04.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:04.710][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[2025-02-05 19:12:04.711][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-02-05 19:12:04.715][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:04.716][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:04.718][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-02-05 19:12:05.095][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-02-05 19:12:05.460][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:05.464][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-02-05 19:12:05.469][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-02-05 19:12:05.474][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-02-05 19:12:05.478][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:12:05.480][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:12:05.482][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:12:05.484][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:05.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:05.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:05.494][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:05.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:05.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:05.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:05.501][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:05.503][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:05.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.505][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:05.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:05.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.512][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:05.513][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:05.515][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.516][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.517][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:05.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:05.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.523][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:05.524][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:05.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.527][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.528][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:05.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:05.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.534][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:05.536][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:05.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.538][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.540][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:05.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:05.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.546][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:05.547][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:05.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.550][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.551][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:05.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:05.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.557][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:05.558][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:05.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.573][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.575][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:05.577][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:05.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.580][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.582][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:05.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:05.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.588][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:05.590][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:05.591][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.593][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.595][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:05.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:05.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.601][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:05.602][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:05.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.605][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.607][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:05.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:05.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.612][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:05.613][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:05.615][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.616][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.618][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:05.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:05.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.623][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:05.625][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:05.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.628][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.631][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:05.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:05.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.644][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:05.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:05.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:05.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:05.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:05.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:05.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:05.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:05.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:05.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:05.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:05.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:05.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:05.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:05.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:05.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:05.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:05.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:05.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:05.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:05.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:05.755][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-02-05 19:12:05.765][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:05.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:05.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.772][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:05.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:05.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:05.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:05.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:05.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:05.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:05.831][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[2025-02-05 19:12:05.851][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:05.853][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:05.858][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-02-05 19:12:06.394][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-02-05 19:12:06.898][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:06.902][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-02-05 19:12:06.921][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-02-05 19:12:06.927][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:06.928][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:06.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:06.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:06.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:06.940][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:06.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:06.943][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:06.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:06.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:06.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:06.948][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:06.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:06.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:06.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:06.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:06.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:06.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:06.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:06.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:06.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:06.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:06.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:06.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:06.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:06.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:06.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:06.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:06.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:06.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:06.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:06.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:06.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:06.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:06.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:06.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:06.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:06.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:06.989][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:06.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:06.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:06.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:06.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:06.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:06.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:06.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:06.999][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:07.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:07.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:07.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:07.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:07.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:07.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:07.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.024][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.030][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.035][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:07.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:07.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:07.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:07.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:07.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:07.053][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:07.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:07.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.071][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:07.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:07.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:07.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:07.112][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:07.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:07.117][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:07.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:07.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.145][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:07.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:07.166][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:07.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:07.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:07.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:07.180][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:07.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:07.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.196][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:07.226][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:07.227][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:07.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:07.239][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:07.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:07.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:07.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:07.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:07.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:07.300][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:07.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:07.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:07.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:07.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:07.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:07.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.333][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:07.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:07.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:07.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:07.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:07.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:07.403][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:07.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:07.406][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.417][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.426][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:07.432][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:07.433][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:07.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:07.448][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:07.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:07.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:07.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:07.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.476][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.485][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:07.523][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:07.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:07.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:07.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:07.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:07.539][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:07.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:07.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.580][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:07.599][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:07.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:07.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:07.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:07.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:07.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:07.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:07.624][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.631][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.638][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:07.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:07.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:07.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:07.675][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:07.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:07.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:07.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:07.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.706][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.720][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:07.729][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:07.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:07.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:07.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:07.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:07.747][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:07.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:07.765][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:07.802][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:07.803][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:07.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:07.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:07.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:07.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:07.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:07.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.844][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:07.882][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:07.884][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:07.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:07.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:07.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:07.906][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:07.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:07.909][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:07.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:07.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:07.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:07.977][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:07.979][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:07.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:08.007][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:08.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:08.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:08.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:08.023][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:08.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:08.030][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:08.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:08.041][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:08.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:08.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:08.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:08.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:08.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:08.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:08.072][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:08.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:08.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:08.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:08.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:08.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:08.113][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:08.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:08.121][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:08.123][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:08.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:08.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:08.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:08.139][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:08.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:08.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:08.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:08.156][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:08.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:08.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:08.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:08.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:08.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:08.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:08.201][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:08.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:08.204][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:08.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:08.207][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:08.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:08.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:08.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:08.239][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:08.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:08.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:08.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:08.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:08.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:08.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:08.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:08.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:08.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:08.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:08.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:08.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:08.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:08.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:08.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:08.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:08.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:08.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:08.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:08.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:08.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:08.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:08.466][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-05 19:12:08.478][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:08.481][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:08.485][private$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[2025-02-05 19:12:08.880][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[2025-02-05 19:12:09.261][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:09.264][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-02-05 19:12:09.270][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-02-05 19:12:09.275][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[2025-02-05 19:12:09.280][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:09.282][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:09.285][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-02-05 19:12:09.675][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-02-05 19:12:10.039][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:10.042][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-02-05 19:12:10.048][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-02-05 19:12:10.053][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:10.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:10.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:10.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:10.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:10.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:10.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:10.070][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-02-05 19:12:10.071][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:12:10.073][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-02-05 19:12:10.075][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:12:10.076][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:12:10.078][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:12:10.079][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:12:10.081][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:12:10.082][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:12:10.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:10.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:10.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:10.096][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:10.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:10.098][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:10.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:10.101][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-02-05 19:12:10.105][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:10.106][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:10.108][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-02-05 19:12:10.550][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-02-05 19:12:10.933][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:10.936][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-02-05 19:12:10.942][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-02-05 19:12:10.946][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-02-05 19:12:10.949][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:12:10.972][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:12:10.974][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:12:10.977][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:10.978][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:10.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:10.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:10.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:10.990][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:10.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:10.994][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:10.995][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:10.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:10.998][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:10.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:11.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:11.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.005][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:11.006][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:11.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.009][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.010][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:11.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:11.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.016][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:11.017][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:11.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.019][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.021][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:11.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:11.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.027][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:11.028][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:11.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.031][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.033][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:11.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:11.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.038][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:11.040][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:11.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.042][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.044][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:11.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:11.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.050][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:11.051][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:11.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.054][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.056][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:11.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:11.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.061][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:11.062][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:11.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.065][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.067][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:11.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:11.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.072][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:11.074][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:11.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.076][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:11.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:11.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.083][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:11.085][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:11.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.087][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.089][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:11.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:11.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.094][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:11.096][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:11.097][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.098][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.100][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:11.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:11.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.105][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:11.107][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:11.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.110][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.112][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:11.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:11.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:11.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:11.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:11.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:11.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:11.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:11.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:11.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:11.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:11.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:11.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:11.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:11.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:11.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:11.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:11.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:11.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:11.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:11.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:11.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:11.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:11.265][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-02-05 19:12:11.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:11.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:11.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:11.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:11.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:11.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:11.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:11.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:11.304][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:11.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:11.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:11.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:11.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:11.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:11.336][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:11.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:11.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.350][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:11.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:11.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:11.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:11.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:11.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:11.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:11.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:11.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:11.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:11.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:11.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:11.382][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:11.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:11.386][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-02-05 19:12:11.388][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:12:11.390][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-02-05 19:12:11.406][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:12:11.412][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:12:11.421][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:12:11.423][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:12:11.425][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:12:11.426][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:12:11.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:11.433][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:11.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:11.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:11.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:11.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:11.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:11.449][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-02-05 19:12:11.461][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:11.464][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:11.467][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-02-05 19:12:11.843][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-02-05 19:12:12.209][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:12.212][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-02-05 19:12:12.218][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-02-05 19:12:12.222][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-02-05 19:12:12.225][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:12:12.227][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:12:12.228][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:12:12.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:12.232][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:12.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:12.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:12.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:12.245][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:12.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:12.250][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:12.252][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:12.253][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.254][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:12.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:12.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.284][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:12.286][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:12.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.289][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.291][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:12.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:12.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.298][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:12.300][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:12.301][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.303][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.305][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:12.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:12.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.311][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:12.313][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:12.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.316][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.318][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:12.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:12.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.324][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:12.325][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:12.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.328][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.330][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:12.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:12.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.336][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:12.337][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:12.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.340][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.341][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:12.343][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:12.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.346][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.347][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:12.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:12.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.353][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.355][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.356][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.357][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.365][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:12.366][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:12.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.369][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.372][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:12.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:12.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.379][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:12.381][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:12.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.385][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.387][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:12.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:12.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.395][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:12.396][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:12.398][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.399][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.401][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:12.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:12.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:12.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:12.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:12.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:12.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:12.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:12.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:12.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:12.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:12.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:12.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:12.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:12.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:12.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:12.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:12.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:12.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:12.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:12.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:12.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:12.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:12.571][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-02-05 19:12:12.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.590][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:12.690][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-05 19:12:12.709][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:12:12.714][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-05 19:12:12.718][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:12:12.736][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-02-05 19:12:12.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:12.760][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:12.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:12.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:12.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:12.785][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:12.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:12.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:12.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:12.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:12.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:12.901][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:12.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:12.906][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:12.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:12.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.924][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.931][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:12.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:12.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:12.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:12.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:12.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:12.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:13.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:13.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:13.005][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:13.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:13.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.039][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.052][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:13.062][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:13.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:13.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:13.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:13.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:13.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:13.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:13.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.111][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.124][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:13.174][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:13.175][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:13.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:13.186][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:13.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:13.189][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:13.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:13.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:13.248][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:13.251][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:13.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:13.277][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:13.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:13.280][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:13.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:13.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:13.309][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:13.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:13.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:13.336][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:13.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:13.339][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:13.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:13.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:13.399][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:13.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:13.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:13.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:13.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:13.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:13.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:13.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.440][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:13.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:13.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:13.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:13.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:13.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:13.498][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:13.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:13.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:13.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:13.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:13.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:13.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:13.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:13.558][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:13.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:13.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.575][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:13.623][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:13.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:13.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:13.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:13.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:13.649][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:13.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:13.652][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:13.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:13.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:13.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:13.692][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:13.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:13.695][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:13.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:13.698][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:13.762][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:13.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:13.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:13.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:13.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:13.780][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:13.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:13.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:13.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:13.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:13.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:13.826][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:13.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:13.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:13.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:13.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.865][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:13.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:13.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:13.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:13.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:13.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:13.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:13.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:13.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:13.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:13.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:13.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:13.991][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:13.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:13.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:14.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:14.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:14.015][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:14.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:14.021][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.028][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:14.053][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:14.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:14.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:14.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:14.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:14.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:14.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:14.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.119][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:14.136][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:14.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:14.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:14.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:14.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:14.164][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:14.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:14.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:14.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:14.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:14.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:14.221][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:14.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:14.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:14.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:14.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.265][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:14.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:14.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:14.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:14.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:14.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:14.309][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:14.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:14.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.350][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:14.424][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-05 19:12:14.435][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:12:14.437][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-05 19:12:14.439][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:12:14.441][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-02-05 19:12:14.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:14.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:14.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:14.496][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:14.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:14.501][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:14.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:14.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.531][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:14.537][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:14.541][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:14.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:14.554][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:14.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:14.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:14.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:14.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:14.640][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:14.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:14.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:14.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:14.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:14.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:14.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:14.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:14.713][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:14.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:14.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:14.774][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:14.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:14.778][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:14.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:14.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.793][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:14.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:14.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:14.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:14.851][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:14.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:14.856][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:14.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:14.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.878][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:14.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:14.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:14.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:14.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:14.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:14.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:14.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:14.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:14.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:14.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:14.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:14.953][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:14.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:14.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:14.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:14.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:14.996][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:14.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:15.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:15.038][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:15.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:15.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:15.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:15.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:15.056][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:15.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:15.059][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.077][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:15.113][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:15.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:15.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:15.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:15.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:15.149][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:15.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:15.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:15.202][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:15.204][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:15.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:15.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:15.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:15.222][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:15.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:15.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:15.271][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:15.273][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:15.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:15.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:15.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:15.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:15.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:15.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:15.348][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:15.352][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:15.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:15.366][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:15.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:15.369][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:15.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:15.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:15.422][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:15.424][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:15.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:15.436][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:15.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:15.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:15.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:15.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:15.495][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:15.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:15.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:15.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:15.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:15.533][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:15.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:15.536][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.555][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:15.574][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:15.576][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:15.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:15.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:15.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:15.611][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:15.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:15.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.646][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:15.659][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:15.660][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:15.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:15.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:15.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:15.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:15.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:15.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.707][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:15.716][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:15.717][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:15.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:15.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:15.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:15.733][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:15.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:15.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:15.793][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:15.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:15.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:15.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:15.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:15.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:15.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:15.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.850][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:15.871][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:15.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:15.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:15.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:15.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:15.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:15.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:15.904][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:15.928][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:15.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:15.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:15.938][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:15.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:15.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:15.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:15.952][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:15.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:15.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:15.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:16.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:16.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:16.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:16.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:16.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:16.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:16.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:16.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:16.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:16.063][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-02-05 19:12:16.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-02-05 19:12:16.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:16.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-05 19:12:16.118][biodb::testThat]
biodb.INFO [2025-02-05 19:12:16.120][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-02-05 19:12:16.122][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:12:16.124][biodb::testThat]
biodb.TRACE[2025-02-05 19:12:16.140][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-05 19:12:16.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-05 19:12:16.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:16.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:16.151][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:16.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:16.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:16.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:16.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:16.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:16.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:16.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:16.166][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:16.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:16.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:16.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:16.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:16.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:16.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:16.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:16.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:16.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:16.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:16.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:16.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:16.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:16.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:16.243][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-05 19:12:16.263][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:16.266][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:16.269][private$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[2025-02-05 19:12:16.636][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[2025-02-05 19:12:17.014][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:17.017][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-02-05 19:12:17.023][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-02-05 19:12:17.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:17.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:17.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:17.041][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:17.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:17.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:17.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:17.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:17.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:17.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:17.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:17.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:17.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:17.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:17.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:17.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:17.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:17.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:17.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:17.070][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[2025-02-05 19:12:17.075][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:17.077][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:17.080][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-02-05 19:12:17.879][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-02-05 19:12:18.248][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:18.251][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-02-05 19:12:18.257][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-02-05 19:12:18.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:18.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:18.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:18.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:18.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:18.277][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:18.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:18.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:18.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:18.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:18.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:18.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:18.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:18.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:18.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:18.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:18.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:18.308][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:18.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:18.312][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:18.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:18.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:18.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:18.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:18.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:18.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.326][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:18.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:18.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:18.332][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-05 19:12:18.334][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:18.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:18.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:18.345][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:18.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:18.347][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:18.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:18.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.361][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:18.362][private$selectFields]
biodb.TRACE[2025-02-05 19:12:18.363][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-05 19:12:18.364][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-05 19:12:18.365][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:18.367][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.368][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.370][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.372][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.373][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.374][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.375][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.377][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:18.378][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:18.379][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.381][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.382][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.383][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.384][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-05 19:12:18.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.417][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-02-05 19:12:18.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:18.422][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:18.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:18.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:18.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:18.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:18.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:18.444][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.453][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.462][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:18.475][private$selectFields]
biodb.TRACE[2025-02-05 19:12:18.478][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-05 19:12:18.482][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-05 19:12:18.485][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:18.488][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.491][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.493][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.495][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.498][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.507][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.512][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.515][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:18.517][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:18.526][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.529][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.530][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.532][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.534][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-05 19:12:18.540][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.583][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-05 19:12:18.594][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:18.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:18.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:18.614][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:18.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:18.619][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:18.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:18.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.651][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.666][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:18.668][private$selectFields]
biodb.TRACE[2025-02-05 19:12:18.671][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-05 19:12:18.673][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-05 19:12:18.675][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:18.686][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.689][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.692][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.699][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.703][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.706][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.709][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.711][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:18.725][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:18.728][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.731][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.748][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.751][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-05 19:12:18.763][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:18.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.807][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-02-05 19:12:18.810][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-05 19:12:18.813][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-05 19:12:18.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:18.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:18.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:18.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:18.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:18.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:18.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:18.924][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:18.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:18.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:18.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:19.147][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:19.149][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:19.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:19.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:19.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:19.164][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:19.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:19.176][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-05 19:12:19.182][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:19.183][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:19.218][private$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[2025-02-05 19:12:19.584][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[2025-02-05 19:12:19.952][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:19.955][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-02-05 19:12:19.961][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-02-05 19:12:19.966][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[2025-02-05 19:12:19.970][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:19.972][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:19.974][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-02-05 19:12:20.339][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-02-05 19:12:20.709][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:20.712][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-02-05 19:12:20.718][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-02-05 19:12:20.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:20.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:20.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:20.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:20.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:20.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:20.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:20.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:20.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:20.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:20.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:20.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:20.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:20.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:20.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:20.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:20.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:20.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:20.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:20.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:20.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:20.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:20.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:20.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:20.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:20.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:20.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:20.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:20.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:20.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:20.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:20.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:20.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:20.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:20.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:20.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:20.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:20.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:20.785][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:20.786][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:20.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:20.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:20.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:20.798][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:20.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:20.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:20.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:20.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:20.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:20.807][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:20.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:20.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:20.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:20.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:20.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:20.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:20.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:20.850][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-05 19:12:20.889][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:20.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:20.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:20.901][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:20.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:20.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:20.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:20.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:20.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:20.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:20.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:20.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:20.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:20.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:20.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:20.927][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:20.928][private$selectFields]
biodb.TRACE[2025-02-05 19:12:20.930][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-05 19:12:20.931][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-05 19:12:20.932][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:20.934][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:20.935][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:20.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:20.943][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:20.945][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:20.947][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:20.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:20.950][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:20.959][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:20.962][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:20.964][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:20.966][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:20.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:20.976][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:20.979][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-05 19:12:20.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:20.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:20.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:20.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:20.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.017][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.025][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-02-05 19:12:21.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:21.032][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:21.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:21.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:21.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:21.048][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:21.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:21.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.106][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.187][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:21.189][private$selectFields]
biodb.TRACE[2025-02-05 19:12:21.191][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-05 19:12:21.193][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-05 19:12:21.209][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:21.211][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.214][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.218][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.220][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.222][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.226][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.229][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:21.282][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:21.285][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.287][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.295][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.298][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-05 19:12:21.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.342][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-05 19:12:21.354][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:21.357][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:21.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:21.402][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:21.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:21.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:21.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:21.411][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.488][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:21.490][private$selectFields]
biodb.TRACE[2025-02-05 19:12:21.504][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-05 19:12:21.507][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-05 19:12:21.509][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:21.512][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.520][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.523][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.525][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.527][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.533][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.535][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:21.537][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:21.538][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.540][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.550][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.552][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-05 19:12:21.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:21.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.586][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-02-05 19:12:21.588][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-05 19:12:21.589][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-05 19:12:21.644][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-02-05 19:12:21.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-02-05 19:12:21.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-05 19:12:21.665][biodb::testThat]
biodb.INFO [2025-02-05 19:12:21.667][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-02-05 19:12:21.669][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:12:21.671][biodb::testThat]
biodb.TRACE[2025-02-05 19:12:21.680][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-05 19:12:21.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-05 19:12:21.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.697][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:21.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:21.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.721][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:21.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:21.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.731][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:21.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:21.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:21.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:21.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:21.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:21.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:21.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:21.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:21.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:21.791][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:21.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:21.804][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-05 19:12:21.817][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:12:21.821][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-02-05 19:12:21.825][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:12:21.840][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-02-05 19:12:21.845][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:21.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:21.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:21.862][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:21.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:21.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:21.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:21.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:21.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:21.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:21.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:21.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.899][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:21.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:21.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:21.914][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-05 19:12:21.924][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:12:21.927][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-02-05 19:12:21.930][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:12:21.932][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-02-05 19:12:21.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:21.938][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:21.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:21.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:21.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:21.952][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:21.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:21.955][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:21.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:21.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:21.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:21.990][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:22.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:22.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.008][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:22.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:22.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:22.025][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:22.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:22.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:22.054][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:22.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:22.058][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:22.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:22.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:22.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:22.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:22.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:22.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.120][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:22.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:22.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:22.144][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-05 19:12:22.152][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:22.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:22.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:22.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:22.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:22.184][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:22.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:22.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.224][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:22.226][private$selectFields]
biodb.TRACE[2025-02-05 19:12:22.229][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-05 19:12:22.232][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-05 19:12:22.244][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:22.248][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.253][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.266][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.269][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.272][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.279][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.281][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.284][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:22.286][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:22.288][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.291][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.294][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.295][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.297][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-05 19:12:22.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.356][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-02-05 19:12:22.359][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:22.372][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:22.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:22.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:22.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:22.404][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:22.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:22.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.447][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:22.450][private$selectFields]
biodb.TRACE[2025-02-05 19:12:22.454][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-05 19:12:22.457][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-05 19:12:22.473][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:22.476][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.479][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.486][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.488][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.491][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.500][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.503][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:22.506][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:22.509][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.520][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.525][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.527][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-05 19:12:22.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.557][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.575][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-05 19:12:22.578][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:22.581][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:22.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:22.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:22.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:22.600][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:22.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:22.617][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.656][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:22.657][private$selectFields]
biodb.TRACE[2025-02-05 19:12:22.664][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-05 19:12:22.666][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-05 19:12:22.669][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:22.671][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.686][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.694][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.699][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.702][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.705][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.708][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.717][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:22.720][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:22.724][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.727][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.737][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.741][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.744][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-05 19:12:22.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.778][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:22.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.790][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-02-05 19:12:22.791][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-05 19:12:22.793][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-05 19:12:22.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:22.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:22.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:22.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:22.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:22.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:22.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:22.865][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:22.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:22.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:22.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:22.884][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:22.886][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:22.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:22.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:22.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:22.913][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:22.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:22.925][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-05 19:12:22.930][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:12:22.932][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-02-05 19:12:22.944][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:12:22.947][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-02-05 19:12:22.953][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-05 19:12:22.967][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:12:22.970][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-02-05 19:12:22.972][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:12:22.978][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-02-05 19:12:22.983][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:22.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:22.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:22.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:23.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:23.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:23.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:23.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:23.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:23.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.019][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:23.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:23.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.039][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:23.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:23.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:23.053][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:23.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:23.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:23.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:23.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:23.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:23.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:23.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:23.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:23.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:23.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:23.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:23.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:23.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:23.106][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:23.118][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:23.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:23.147][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:23.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:23.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:23.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:23.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:23.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:23.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:23.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:23.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:23.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:23.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:23.184][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-05 19:12:23.196][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:23.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:23.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:23.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:23.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:23.220][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:23.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:23.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.252][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:23.254][private$selectFields]
biodb.TRACE[2025-02-05 19:12:23.256][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-05 19:12:23.257][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-05 19:12:23.259][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:23.261][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.263][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.266][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.279][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.280][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.282][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.283][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.285][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:23.286][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:23.292][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.294][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.296][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.297][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.299][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-05 19:12:23.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.359][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-02-05 19:12:23.362][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:23.364][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:23.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:23.379][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:23.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:23.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:23.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:23.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.411][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:23.412][private$selectFields]
biodb.TRACE[2025-02-05 19:12:23.413][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-05 19:12:23.415][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-05 19:12:23.416][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:23.427][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.429][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.431][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.433][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.434][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.443][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.445][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:23.446][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:23.448][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.449][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.470][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.473][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-05 19:12:23.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.498][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.508][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.517][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-05 19:12:23.524][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:23.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:23.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:23.537][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:23.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:23.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:23.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:23.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.557][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.571][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:23.573][private$selectFields]
biodb.TRACE[2025-02-05 19:12:23.575][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-05 19:12:23.576][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-05 19:12:23.578][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:23.580][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.601][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.608][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.610][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.612][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.634][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.637][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:23.639][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:23.641][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.643][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.646][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.648][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-05 19:12:23.649][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.676][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:23.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.695][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-02-05 19:12:23.697][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-05 19:12:23.698][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-05 19:12:23.720][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-02-05 19:12:23.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-02-05 19:12:23.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-05 19:12:23.742][biodb::testThat]
biodb.INFO [2025-02-05 19:12:23.744][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-02-05 19:12:23.746][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:12:23.747][biodb::testThat]
biodb.TRACE[2025-02-05 19:12:23.763][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-05 19:12:23.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-05 19:12:23.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.771][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:23.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:23.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.781][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:23.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:23.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:23.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:23.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:23.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:23.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:23.830][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:23.832][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:23.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:23.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:23.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:23.856][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:23.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:23.877][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-05 19:12:23.901][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:12:23.904][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-02-05 19:12:23.914][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:12:23.916][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-02-05 19:12:23.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:23.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:23.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:23.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:23.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:23.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:23.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:23.951][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:23.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:23.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.971][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:23.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:23.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:23.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:23.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:23.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:23.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:23.992][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-05 19:12:23.996][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:12:24.006][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-02-05 19:12:24.008][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:12:24.019][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-02-05 19:12:24.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:24.025][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:24.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:24.052][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:24.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:24.055][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:24.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:24.058][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:24.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:24.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.064][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:24.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:24.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:24.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:24.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:24.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:24.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:24.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:24.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:24.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:24.125][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:24.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:24.138][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:24.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:24.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.151][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:24.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:24.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:24.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:24.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:24.175][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-05 19:12:24.177][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:24.179][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:24.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:24.188][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:24.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:24.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:24.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:24.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.246][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:24.248][private$selectFields]
biodb.TRACE[2025-02-05 19:12:24.250][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-05 19:12:24.253][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-05 19:12:24.267][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:24.270][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.272][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.276][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.277][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.286][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.288][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.289][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.292][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:24.294][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:24.303][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.305][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.309][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.310][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-05 19:12:24.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.323][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.358][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-02-05 19:12:24.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:24.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:24.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:24.374][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:24.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:24.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:24.380][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[2025-02-05 19:12:24.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.402][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:24.404][private$selectFields]
biodb.TRACE[2025-02-05 19:12:24.406][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-05 19:12:24.407][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-05 19:12:24.419][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:24.421][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.423][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.426][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.427][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.429][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.446][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.450][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.451][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:24.453][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:24.454][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.465][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.472][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.475][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-05 19:12:24.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.530][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-05 19:12:24.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:24.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:24.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:24.545][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:24.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:24.548][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:24.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:24.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.577][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:24.578][private$selectFields]
biodb.TRACE[2025-02-05 19:12:24.580][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-05 19:12:24.581][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-05 19:12:24.583][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:24.584][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.605][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.609][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.611][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.614][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.621][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.624][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:24.626][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:24.628][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.630][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.646][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.647][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.649][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-05 19:12:24.651][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.686][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:24.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.693][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-02-05 19:12:24.695][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-05 19:12:24.701][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-05 19:12:24.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:24.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:24.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:24.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:24.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:24.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:24.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:24.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:24.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:24.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:24.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:24.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:24.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:24.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:24.829][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:24.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:24.848][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-05 19:12:24.855][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:12:24.865][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-02-05 19:12:24.868][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:12:24.870][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-02-05 19:12:24.891][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-05 19:12:24.897][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:12:24.899][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-02-05 19:12:24.906][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:12:24.909][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-02-05 19:12:24.913][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:24.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:24.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:24.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:24.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:24.933][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:24.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:24.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:24.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:24.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:24.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:24.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:24.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:24.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:24.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:24.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:24.974][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:24.975][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:24.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:25.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:25.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:25.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:25.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:25.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:25.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:25.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:25.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:25.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:25.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:25.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:25.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:25.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:25.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:25.074][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:25.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:25.078][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:25.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:25.081][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:25.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:25.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:25.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:25.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.127][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:25.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:25.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:25.146][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-05 19:12:25.149][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:25.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:25.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:25.160][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:25.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:25.162][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:25.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:25.165][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.184][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:25.190][private$selectFields]
biodb.TRACE[2025-02-05 19:12:25.192][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-05 19:12:25.193][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-05 19:12:25.194][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:25.196][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.197][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.206][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.208][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.210][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.212][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.214][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.215][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:25.216][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:25.224][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.226][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.230][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.232][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-05 19:12:25.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.255][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.276][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-02-05 19:12:25.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:25.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:25.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:25.299][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:25.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:25.302][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:25.303][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[2025-02-05 19:12:25.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.332][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:25.335][private$selectFields]
biodb.TRACE[2025-02-05 19:12:25.337][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-05 19:12:25.339][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-05 19:12:25.341][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:25.343][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.359][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.362][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.365][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.367][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.369][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.372][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.391][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.394][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:25.396][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:25.397][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.399][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.403][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.405][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.406][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-05 19:12:25.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.439][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-05 19:12:25.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:25.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:25.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:25.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:25.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:25.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:25.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:25.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.503][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:25.505][private$selectFields]
biodb.TRACE[2025-02-05 19:12:25.506][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-05 19:12:25.508][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-05 19:12:25.510][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:25.512][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.514][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.516][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.517][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.518][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.520][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.528][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.529][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:25.530][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-05 19:12:25.532][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.533][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.534][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.545][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.547][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-05 19:12:25.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:25.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:25.581][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-02-05 19:12:25.583][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-05 19:12:25.585][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-05 19:12:25.639][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-02-05 19:12:25.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-02-05 19:12:25.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:25.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-05 19:12:25.672][biodb::testThat]
biodb.INFO [2025-02-05 19:12:25.673][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-02-05 19:12:25.675][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:12:25.676][biodb::testThat]
biodb.DEBUG[2025-02-05 19:12:25.679][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-02-05 19:12:25.688][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:12:25.691][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-02-05 19:12:25.693][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:12:25.695][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:12:25.701][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:12:25.704][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:12:25.707][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:12:25.709][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:12:25.724][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:25.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:25.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:25.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:25.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:25.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:25.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:25.747][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-02-05 19:12:25.764][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:25.766][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:25.769][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-02-05 19:12:26.140][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-02-05 19:12:26.740][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:26.742][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-02-05 19:12:26.746][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-02-05 19:12:26.749][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-02-05 19:12:26.750][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:12:26.752][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:12:26.753][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:12:26.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:26.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:26.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:26.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:26.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:26.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:26.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:26.769][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:26.770][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:26.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:26.773][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:26.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:26.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:26.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:26.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:26.779][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:26.780][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:26.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:26.783][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:26.785][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:26.786][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:26.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:26.788][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:26.790][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:26.791][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:26.792][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:26.793][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:26.795][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:26.796][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:26.796][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:26.798][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:26.799][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:26.800][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:26.801][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:26.802][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:26.803][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:26.804][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:26.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:26.807][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:26.808][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:26.810][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:26.811][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:26.812][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:26.814][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:26.815][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:26.816][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:26.818][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:26.819][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:26.821][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:26.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:26.823][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:26.824][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:26.825][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:26.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:26.827][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:26.829][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:26.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:26.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:26.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:26.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:26.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:26.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:26.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:26.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:26.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:26.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:26.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:26.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:26.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:26.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:26.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:26.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:26.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:26.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:26.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:26.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:26.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:26.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:26.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:26.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:26.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:26.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:26.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:26.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:26.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:26.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:26.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:26.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:26.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:26.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:26.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:26.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:26.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:26.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:26.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:26.884][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-02-05 19:12:26.885][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-02-05 19:12:26.897][biodb::testThat]
biodb.INFO [2025-02-05 19:12:26.898][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-02-05 19:12:26.900][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:12:26.901][biodb::testThat]
biodb.DEBUG[2025-02-05 19:12:26.910][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-02-05 19:12:26.912][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-02-05 19:12:26.913][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-02-05 19:12:26.915][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-02-05 19:12:26.917][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-02-05 19:12:26.918][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:12:26.920][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:12:26.921][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:12:26.922][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:12:26.923][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:12:26.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:26.930][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:26.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:26.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:26.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:26.940][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:26.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:26.942][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-02-05 19:12:26.945][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:26.946][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:26.948][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-02-05 19:12:27.304][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-02-05 19:12:27.662][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:27.664][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-02-05 19:12:27.669][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-02-05 19:12:27.671][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:27.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:27.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:27.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:27.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:27.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:27.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:27.686][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-02-05 19:12:27.690][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:27.691][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:27.692][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-02-05 19:12:28.056][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-02-05 19:12:28.423][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:28.426][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-02-05 19:12:28.431][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-02-05 19:12:28.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:28.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:28.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:28.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:28.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:28.445][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:28.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:28.448][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-02-05 19:12:28.451][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:28.453][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:28.455][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-02-05 19:12:28.831][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-02-05 19:12:29.202][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:29.205][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-02-05 19:12:29.211][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-02-05 19:12:29.215][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-02-05 19:12:29.218][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:12:29.220][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-02-05 19:12:29.222][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-02-05 19:12:29.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:29.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:29.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:29.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:29.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:29.237][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:29.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:29.241][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:29.242][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:29.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.245][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:29.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:29.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.251][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:29.253][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:29.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.255][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.257][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:29.258][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:29.259][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.260][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.262][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:29.264][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:29.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.266][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.268][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:29.269][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:29.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.271][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.273][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:29.274][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:29.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.277][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.279][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:29.280][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:29.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.282][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.284][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:29.285][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:29.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.288][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.290][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:29.291][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:29.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.294][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.296][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:29.297][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:29.298][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.300][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.302][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:29.303][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:29.305][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.306][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:29.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:29.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:29.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:29.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:29.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:29.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:29.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:29.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:29.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:29.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:29.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:29.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:29.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:29.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:29.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:29.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:29.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:29.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:29.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:29.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:29.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:29.361][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:29.363][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:29.364][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.366][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:29.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:29.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.373][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:29.374][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:29.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.377][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.379][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:29.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:29.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.387][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:29.388][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:29.389][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.391][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.393][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:29.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:29.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.403][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:29.404][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:29.406][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.407][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.415][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:29.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:29.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.422][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:29.423][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:29.426][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.427][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.428][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:29.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:29.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.434][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:29.439][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:29.440][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.442][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.444][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:29.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:29.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.458][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:29.461][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:29.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.465][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.475][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:29.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:29.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.484][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:29.486][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:29.488][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.491][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.493][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:29.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:29.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.501][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:29.503][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:29.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.506][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.508][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:29.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:29.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.533][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:29.535][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:29.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.540][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.542][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:29.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:29.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.548][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:29.597][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:29.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.602][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.612][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:29.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:29.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:29.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:29.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:29.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:29.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:29.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:29.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:29.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:29.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:29.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:29.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:29.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:29.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:29.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:29.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:29.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:29.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:29.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:29.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:29.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:29.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:29.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-05 19:12:29.750][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:29.754][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:29.756][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.758][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:29.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:29.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.767][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:29.769][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:29.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.778][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.780][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:29.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:29.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.786][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:29.788][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:29.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.805][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.807][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:29.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:29.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.822][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:29.824][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:29.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.827][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.830][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:29.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:29.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.847][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:29.848][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:29.856][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.859][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.861][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:29.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:29.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.869][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:29.871][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:29.873][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.875][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.877][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:29.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:29.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.897][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:29.908][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:29.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.912][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.916][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:29.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:29.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.928][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:29.929][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:29.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.939][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:29.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:29.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.950][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:29.952][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:29.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.955][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.961][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:29.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:29.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.971][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:29.973][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:29.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.980][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:29.982][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:29.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:29.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:29.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:30.002][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:30.004][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:30.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:30.008][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:30.011][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:30.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:30.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:30.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:30.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:30.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:30.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:30.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:30.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:30.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:30.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:30.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:30.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:30.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:30.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:30.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:30.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:30.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:30.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:30.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:30.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:30.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:30.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:30.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:30.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:30.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:30.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:30.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:30.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:30.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:30.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:30.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:30.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:30.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:30.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:30.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:30.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:30.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:30.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:30.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:30.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:30.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:30.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:30.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:30.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:30.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:30.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:30.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:30.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:30.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:30.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:30.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:30.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:30.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:30.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:30.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:30.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:30.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:30.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:30.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:30.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:30.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:30.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:30.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:30.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:30.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:30.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:30.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:30.260][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-02-05 19:12:30.263][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-02-05 19:12:30.264][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-02-05 19:12:30.291][biodb::testThat]
biodb.INFO [2025-02-05 19:12:30.293][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-02-05 19:12:30.294][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:12:30.296][biodb::testThat]
biodb.INFO [2025-02-05 19:12:30.384][biodb::testThat]
biodb.INFO [2025-02-05 19:12:30.387][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-02-05 19:12:30.389][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:12:30.391][biodb::testThat]
biodb.INFO [2025-02-05 19:12:30.424][biodb::testThat]
biodb.INFO [2025-02-05 19:12:30.425][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-02-05 19:12:30.427][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:12:30.428][biodb::testThat]
biodb.DEBUG[2025-02-05 19:12:30.437][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2025-02-05 19:12:30.442][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:30.444][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:30.462][private$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[2025-02-05 19:12:30.891][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[2025-02-05 19:12:31.402][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:31.405][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-02-05 19:12:31.412][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-02-05 19:12:31.431][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:31.433][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:31.434][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:31.435][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:31.437][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:31.438][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:31.440][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:31.441][ef$get] fields variable is a list.
biodb.INFO [2025-02-05 19:12:31.443][biodb::testThat]
biodb.INFO [2025-02-05 19:12:31.444][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2025-02-05 19:12:31.446][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:12:31.447][biodb::testThat]
biodb.ERROR[2025-02-05 19:12:31.467][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-02-05 19:12:31.490][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-02-05 19:12:31.523][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-05 19:12:31.524][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-02-05 19:12:31.526][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-02-05 19:12:31.527][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-05 19:12:31.529][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:31.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:31.531][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:31.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:31.533][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:31.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-02-05 19:12:31.549][biodb::testContext]
biodb.INFO [2025-02-05 19:12:31.550][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-05 19:12:31.552][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-02-05 19:12:31.553][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-05 19:12:31.554][biodb::testContext]
biodb.INFO [2025-02-05 19:12:31.557][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-05 19:12:31.560][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-02-05 19:12:31.565][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-05 19:12:31.567][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-05 19:12:31.568][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-05 19:12:31.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:31.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:31.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:31.573][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-05 19:12:31.574][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-05 19:12:31.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:31.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:31.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:31.579][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-05 19:12:31.580][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-05 19:12:31.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:31.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:31.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:31.585][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-05 19:12:31.586][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-05 19:12:31.587][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-05 19:12:31.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:31.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:31.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:31.592][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-05 19:12:31.594][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-05 19:12:31.596][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-05 19:12:31.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:31.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:31.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:31.601][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-05 19:12:31.616][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-05 19:12:31.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:31.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:31.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:31.627][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-05 19:12:31.629][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-05 19:12:31.631][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-05 19:12:31.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:31.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:31.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:31.638][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-05 19:12:31.641][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-05 19:12:31.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:31.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:31.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:31.654][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-05 19:12:31.656][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-05 19:12:31.657][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-05 19:12:31.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:31.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:31.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:31.666][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-05 19:12:31.668][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-05 19:12:31.669][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-05 19:12:31.671][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-05 19:12:31.672][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-05 19:12:31.673][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-05 19:12:31.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:31.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:31.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:31.683][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-05 19:12:31.685][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-05 19:12:31.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:31.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:31.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:31.690][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-05 19:12:31.704][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-05 19:12:31.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:31.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:31.710][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[2025-02-05 19:12:31.713][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-05 19:12:31.716][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-05 19:12:31.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:31.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:31.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:31.723][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-05 19:12:31.725][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-05 19:12:31.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:31.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:31.730][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[2025-02-05 19:12:31.732][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-05 19:12:31.734][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-05 19:12:31.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:31.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:31.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:31.764][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-05 19:12:31.766][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-05 19:12:31.805][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-05 19:12:31.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:31.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:31.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:31.811][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-05 19:12:31.813][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-05 19:12:31.814][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-05 19:12:31.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:31.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:31.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:31.819][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-05 19:12:31.821][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:31.853][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-05 19:12:31.855][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:31.857][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-05 19:12:31.859][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:31.862][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-05 19:12:31.874][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:31.877][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-05 19:12:31.880][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-05 19:12:31.882][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-05 19:12:31.884][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:31.894][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-05 19:12:31.896][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-05 19:12:31.897][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:31.899][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:31.900][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-05 19:12:31.900][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-05 19:12:31.900][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-05 19:12:31.900][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-05 19:12:31.900][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-05 19:12:31.902][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-05 19:12:31.903][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:31.905][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:31.906][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-05 19:12:31.907][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:31.908][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:31.909][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-05 19:12:31.911][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:31.912][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-05 19:12:31.920][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-05 19:12:31.922][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:31.923][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:31.925][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-05 19:12:31.927][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:31.932][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-05 19:12:31.934][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:31.935][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-05 19:12:31.937][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:31.939][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-05 19:12:31.940][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:31.941][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-05 19:12:31.952][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-05 19:12:31.954][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-05 19:12:31.957][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:31.959][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-05 19:12:31.961][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-05 19:12:31.971][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:31.974][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:31.976][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-05 19:12:31.976][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-05 19:12:31.976][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-05 19:12:31.976][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-05 19:12:31.976][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-05 19:12:31.978][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-05 19:12:31.980][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:31.982][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:31.984][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-05 19:12:31.986][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:31.987][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:31.989][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-05 19:12:31.991][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:31.993][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-05 19:12:31.994][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-05 19:12:31.996][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:31.998][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:32.000][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-05 19:12:32.003][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:32.012][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-05 19:12:32.015][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:32.017][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-05 19:12:32.019][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:32.022][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-05 19:12:32.030][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:32.032][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-05 19:12:32.034][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-05 19:12:32.035][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-05 19:12:32.037][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:32.038][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-05 19:12:32.039][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-05 19:12:32.043][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:32.044][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:32.046][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:32.047][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-05 19:12:32.049][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:32.050][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:32.051][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-05 19:12:32.062][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:32.065][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:32.067][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-05 19:12:32.069][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:32.070][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-05 19:12:32.072][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-05 19:12:32.085][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:32.088][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:32.091][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-05 19:12:32.096][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:32.111][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-05 19:12:32.113][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:32.116][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-05 19:12:32.118][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:32.130][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-05 19:12:32.133][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:32.136][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-05 19:12:32.138][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-05 19:12:32.141][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-05 19:12:32.147][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:32.149][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-05 19:12:32.150][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-05 19:12:32.152][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:32.154][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:32.156][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:32.160][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-05 19:12:32.162][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:32.163][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:32.165][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-05 19:12:32.166][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:32.167][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:32.177][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-05 19:12:32.179][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:32.181][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-05 19:12:32.183][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-05 19:12:32.184][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:32.190][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:32.194][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-05 19:12:32.196][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:32.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:32.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:32.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:32.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:32.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:32.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:32.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:32.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:32.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:32.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:32.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:32.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:32.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:32.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:32.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:32.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:32.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:32.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:32.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:32.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.291][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[2025-02-05 19:12:32.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:32.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:32.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:32.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:32.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:32.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:32.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:32.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:32.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:32.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:32.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:32.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:32.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:32.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:32.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:32.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.335][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[2025-02-05 19:12:32.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:32.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:32.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:32.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.344][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[2025-02-05 19:12:32.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:32.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:32.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:32.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:32.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:32.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:32.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:32.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:32.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:32.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:32.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:32.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:32.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:32.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:32.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:32.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.425][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[2025-02-05 19:12:32.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:32.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:32.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:32.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.450][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[2025-02-05 19:12:32.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:32.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:32.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:32.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:32.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:32.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:32.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:32.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.477][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[2025-02-05 19:12:32.479][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-05 19:12:32.482][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-05 19:12:32.484][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-05 19:12:32.487][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-05 19:12:32.490][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-05 19:12:32.493][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-05 19:12:32.496][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-05 19:12:32.515][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-05 19:12:32.519][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-05 19:12:32.525][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-05 19:12:32.532][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-05 19:12:32.535][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-05 19:12:32.538][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-05 19:12:32.545][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-05 19:12:32.548][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-05 19:12:32.551][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-05 19:12:32.554][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-05 19:12:32.563][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-05 19:12:32.567][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-05 19:12:32.570][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-05 19:12:32.582][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-05 19:12:32.589][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-05 19:12:32.594][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-05 19:12:32.600][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-05 19:12:32.603][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-05 19:12:32.607][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-05 19:12:32.620][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-05 19:12:32.626][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-05 19:12:32.630][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-05 19:12:32.640][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-05 19:12:32.644][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-05 19:12:32.648][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-05 19:12:32.656][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-05 19:12:32.659][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-05 19:12:32.662][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-05 19:12:32.669][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-05 19:12:32.672][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-05 19:12:32.675][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-05 19:12:32.684][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-05 19:12:32.687][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-05 19:12:32.689][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-05 19:12:32.701][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-05 19:12:32.705][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-05 19:12:32.708][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-05 19:12:32.711][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-05 19:12:32.714][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-05 19:12:32.717][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-05 19:12:32.720][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-05 19:12:32.723][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-05 19:12:32.726][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-05 19:12:32.729][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-05 19:12:32.732][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-05 19:12:32.742][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-05 19:12:32.746][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-05 19:12:32.749][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-05 19:12:32.755][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-05 19:12:32.758][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-05 19:12:32.762][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-05 19:12:32.764][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-05 19:12:32.773][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-05 19:12:32.776][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-05 19:12:32.778][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-05 19:12:32.781][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-05 19:12:32.783][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-05 19:12:32.785][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-05 19:12:32.787][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-05 19:12:32.789][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-05 19:12:32.791][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-05 19:12:32.793][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-05 19:12:32.815][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-05 19:12:32.819][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-05 19:12:32.823][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-05 19:12:32.833][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-05 19:12:32.837][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-05 19:12:32.841][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-05 19:12:32.845][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-05 19:12:32.848][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-05 19:12:32.850][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-05 19:12:32.853][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-05 19:12:32.856][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-05 19:12:32.868][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-05 19:12:32.873][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-05 19:12:32.876][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-05 19:12:32.880][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-05 19:12:32.891][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-05 19:12:32.893][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-05 19:12:32.895][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:32.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:32.899][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:32.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:32.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:32.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:32.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:32.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:32.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:32.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:32.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:32.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:32.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:32.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:32.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:32.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:32.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:32.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:32.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:32.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:32.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.955][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[2025-02-05 19:12:32.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:32.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:32.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:32.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:32.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:32.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:32.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:32.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:32.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:32.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:32.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:33.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:33.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:33.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:33.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:33.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:33.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:33.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:33.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:33.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:33.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:33.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:33.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:33.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:33.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:33.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:33.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:33.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:33.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:33.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:33.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:33.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:33.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:33.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:33.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:33.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:33.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:33.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:33.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:33.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:33.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:33.090][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[2025-02-05 19:12:33.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:33.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:33.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:33.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:33.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:33.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:33.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:33.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:33.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:33.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:33.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:33.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:33.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:33.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:33.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:33.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:33.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:33.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:33.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:33.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:33.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:33.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:33.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:33.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:33.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:33.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:33.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:33.181][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.DEBUG[2025-02-05 19:12:33.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:33.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:33.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:33.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:33.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:33.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:33.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:33.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:33.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:33.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:33.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:33.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:33.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:33.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:33.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:33.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:33.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:33.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:33.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:33.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:33.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:33.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:33.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:33.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:33.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:33.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:33.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:33.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:33.282][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-02-05 19:12:33.285][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-02-05 19:12:33.288][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:33.289][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-05 19:12:33.291][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:33.293][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-05 19:12:33.299][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:33.302][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-05 19:12:33.303][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:33.305][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-02-05 19:12:33.307][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-05 19:12:33.316][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-05 19:12:33.319][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:33.320][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-02-05 19:12:33.321][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-05 19:12:33.322][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-02-05 19:12:33.322][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-02-05 19:12:33.322][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-02-05 19:12:33.322][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-02-05 19:12:33.322][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-02-05 19:12:33.322][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-02-05 19:12:33.322][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-02-05 19:12:33.322][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-02-05 19:12:33.322][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-02-05 19:12:33.322][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-02-05 19:12:33.322][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-02-05 19:12:33.323][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:33.324][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-05 19:12:33.324][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-05 19:12:33.324][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-05 19:12:33.325][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-05 19:12:33.325][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:33.326][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:33.328][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-05 19:12:33.331][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:33.333][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:33.335][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-05 19:12:33.336][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:12:33.336][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-02-05 19:12:33.338][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-05 19:12:33.339][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-05 19:12:33.341][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:33.342][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-02-05 19:12:33.342][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-02-05 19:12:33.344][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-05 19:12:33.346][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-05 19:12:33.348][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-02-05 19:12:33.350][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-05 19:12:33.353][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-05 19:12:33.360][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-05 19:12:33.365][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-02-05 19:12:33.367][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-02-05 19:12:33.369][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-02-05 19:12:33.372][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-02-05 19:12:33.375][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-05 19:12:33.376][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-05 19:12:33.377][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-02-05 19:12:33.379][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-02-05 19:12:33.380][biodb::testThat]
biodb.INFO [2025-02-05 19:12:33.383][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2025-02-05 19:12:33.384][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:12:33.385][biodb::testThat]
biodb.DEBUG[2025-02-05 19:12:33.389][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-02-05 19:12:33.393][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:33.394][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:33.395][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-02-05 19:12:33.751][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-02-05 19:12:34.274][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:34.278][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-02-05 19:12:34.284][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-02-05 19:12:34.290][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-05 19:12:34.294][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:34.296][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:34.298][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-02-05 19:12:34.663][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-02-05 19:12:35.019][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:35.023][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-02-05 19:12:35.029][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-02-05 19:12:35.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:35.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:35.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:35.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:35.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:35.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:35.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:35.049][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[2025-02-05 19:12:35.053][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:35.055][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:35.057][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-02-05 19:12:35.419][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-02-05 19:12:35.800][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:35.804][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-02-05 19:12:35.810][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-02-05 19:12:35.813][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:35.815][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:35.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:35.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:35.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:35.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:35.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:35.854][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:35.855][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:35.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:35.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:35.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:35.868][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:35.870][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[2025-02-05 19:12:35.878][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-05 19:12:35.882][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:12:35.884][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-02-05 19:12:35.886][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:12:35.888][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-02-05 19:12:35.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:35.891][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:35.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:35.901][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:35.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:35.905][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:35.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:35.909][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-05 19:12:35.914][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:12:35.917][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-02-05 19:12:35.919][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:12:35.921][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-02-05 19:12:35.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:35.926][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:35.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:35.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:35.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:35.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:35.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:35.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:35.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:35.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:35.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:35.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:35.961][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:35.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:35.969][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-05 19:12:35.974][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:12:35.979][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-02-05 19:12:35.982][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:12:35.985][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-02-05 19:12:35.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:35.995][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:35.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:36.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:36.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:36.015][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:36.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:36.028][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-05 19:12:36.034][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:12:36.042][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-02-05 19:12:36.045][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:12:36.047][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-02-05 19:12:36.058][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:36.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:36.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:36.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:36.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:36.076][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:36.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:36.099][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-05 19:12:36.119][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:36.123][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:36.127][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-02-05 19:12:36.516][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-02-05 19:12:36.879][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:36.883][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-02-05 19:12:36.889][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-02-05 19:12:36.892][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:36.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:36.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:36.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:36.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:36.906][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:36.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-02-05 19:12:36.916][biodb::testThat]
biodb.INFO [2025-02-05 19:12:36.918][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2025-02-05 19:12:36.919][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:12:36.920][biodb::testThat]
biodb.DEBUG[2025-02-05 19:12:36.924][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[2025-02-05 19:12:36.927][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:36.928][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:36.930][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-02-05 19:12:37.303][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-02-05 19:12:37.696][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:37.700][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-02-05 19:12:37.704][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-02-05 19:12:37.706][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:37.707][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:37.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:37.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:37.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:37.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:37.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:37.725][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-05 19:12:37.729][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:37.730][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:37.732][private$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[2025-02-05 19:12:38.103][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[2025-02-05 19:12:38.453][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:38.455][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-02-05 19:12:38.458][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-02-05 19:12:38.471][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:38.472][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:38.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:38.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:38.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:38.479][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:38.480][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.INFO [2025-02-05 19:12:38.485][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-05 19:12:38.486][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-02-05 19:12:38.497][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-02-05 19:12:38.498][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-05 19:12:38.498][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:38.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:38.500][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:38.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:38.501][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:38.502][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.INFO [2025-02-05 19:12:38.506][biodb::testContext]
biodb.INFO [2025-02-05 19:12:38.507][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-05 19:12:38.507][biodb::testContext] Test context - Test web services
biodb.INFO [2025-02-05 19:12:38.508][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-05 19:12:38.509][biodb::testContext]
biodb.INFO [2025-02-05 19:12:38.510][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-05 19:12:38.512][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-02-05 19:12:38.515][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-05 19:12:38.517][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-05 19:12:38.518][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-05 19:12:38.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:38.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:38.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:38.521][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-05 19:12:38.521][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-05 19:12:38.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:38.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:38.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:38.524][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-05 19:12:38.525][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-05 19:12:38.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:38.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:38.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:38.528][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-05 19:12:38.543][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-05 19:12:38.544][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-05 19:12:38.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:38.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:38.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:38.548][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-05 19:12:38.549][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-05 19:12:38.550][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-05 19:12:38.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:38.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:38.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:38.601][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-05 19:12:38.602][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-05 19:12:38.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:38.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:38.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:38.605][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-05 19:12:38.606][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-05 19:12:38.607][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-05 19:12:38.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:38.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:38.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:38.610][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-05 19:12:38.612][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-05 19:12:38.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:38.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:38.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:38.616][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-05 19:12:38.616][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-05 19:12:38.617][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-05 19:12:38.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:38.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:38.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:38.620][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-05 19:12:38.621][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-05 19:12:38.622][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-05 19:12:38.623][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-05 19:12:38.624][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-05 19:12:38.625][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-05 19:12:38.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:38.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:38.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:38.628][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-05 19:12:38.629][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-05 19:12:38.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:38.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:38.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:38.631][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-05 19:12:38.632][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-05 19:12:38.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:38.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:38.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:38.635][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-05 19:12:38.636][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-05 19:12:38.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:38.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:38.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:38.639][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-05 19:12:38.640][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-05 19:12:38.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:38.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:38.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:38.644][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-05 19:12:38.645][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-05 19:12:38.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:38.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:38.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:38.660][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-05 19:12:38.660][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-05 19:12:38.857][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-05 19:12:38.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:38.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:38.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:38.860][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-05 19:12:38.861][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-05 19:12:38.862][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-05 19:12:38.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:38.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:38.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:38.866][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-05 19:12:38.867][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:38.868][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-05 19:12:38.869][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:38.869][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-05 19:12:38.870][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:38.871][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-05 19:12:38.872][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:38.873][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-05 19:12:38.874][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-05 19:12:38.875][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-05 19:12:38.876][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:38.877][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-05 19:12:38.878][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-05 19:12:38.879][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:38.881][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:38.882][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-05 19:12:38.882][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-05 19:12:38.882][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-05 19:12:38.882][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-05 19:12:38.882][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-05 19:12:38.883][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-05 19:12:38.884][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:38.885][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:38.886][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-05 19:12:38.887][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:38.888][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:38.889][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-05 19:12:38.890][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:38.891][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-05 19:12:38.892][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-05 19:12:38.893][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:38.893][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:38.895][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-05 19:12:38.897][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:38.899][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-05 19:12:38.900][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:38.901][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-05 19:12:38.902][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:38.902][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-05 19:12:38.903][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:38.904][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-05 19:12:38.905][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-05 19:12:38.906][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-05 19:12:38.907][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:38.907][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-05 19:12:38.908][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-05 19:12:38.909][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:38.911][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:38.912][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-05 19:12:38.912][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-05 19:12:38.912][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-05 19:12:38.912][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-05 19:12:38.912][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-05 19:12:38.913][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-05 19:12:38.914][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:38.914][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:38.915][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-05 19:12:38.916][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:38.917][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:38.917][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-05 19:12:38.919][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:38.919][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-05 19:12:38.921][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-05 19:12:38.922][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:38.923][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:38.924][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-05 19:12:38.925][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:38.926][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-05 19:12:38.927][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:38.928][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-05 19:12:38.929][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:38.930][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-05 19:12:38.936][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:38.938][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-05 19:12:38.939][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-05 19:12:38.940][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-05 19:12:38.940][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:38.941][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-05 19:12:38.942][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-05 19:12:38.943][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:38.944][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:38.945][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:38.946][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-05 19:12:38.947][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:38.948][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:38.948][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-05 19:12:38.949][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:38.950][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:38.951][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-05 19:12:38.952][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:38.953][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-05 19:12:38.953][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-05 19:12:38.954][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:38.955][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:38.956][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-05 19:12:38.957][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:38.958][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-05 19:12:38.959][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:38.959][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-05 19:12:38.960][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:38.961][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-05 19:12:38.962][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:38.963][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-05 19:12:38.964][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-05 19:12:38.965][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-05 19:12:38.966][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:38.967][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-05 19:12:38.967][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-05 19:12:38.968][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:38.969][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:38.970][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:38.971][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-05 19:12:38.972][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:38.973][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:38.973][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-05 19:12:38.974][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:38.975][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:38.978][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-05 19:12:38.978][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:38.979][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-05 19:12:38.980][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-05 19:12:38.981][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:38.982][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:38.983][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-05 19:12:38.983][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:38.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:38.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:38.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:38.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:38.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:38.988][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[2025-02-05 19:12:38.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:38.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:38.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:38.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:38.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:38.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:38.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:39.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:39.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:39.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:39.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:39.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:39.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.040][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[2025-02-05 19:12:39.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:39.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.060][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.DEBUG[2025-02-05 19:12:39.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.064][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[2025-02-05 19:12:39.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.068][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[2025-02-05 19:12:39.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.072][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[2025-02-05 19:12:39.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.075][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[2025-02-05 19:12:39.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.080][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[2025-02-05 19:12:39.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:39.084][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-05 19:12:39.085][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-05 19:12:39.086][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-05 19:12:39.087][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-05 19:12:39.089][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-05 19:12:39.090][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-05 19:12:39.091][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-05 19:12:39.092][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-05 19:12:39.093][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-05 19:12:39.094][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-05 19:12:39.095][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-05 19:12:39.096][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-05 19:12:39.097][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-05 19:12:39.098][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-05 19:12:39.100][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-05 19:12:39.102][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-05 19:12:39.103][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-05 19:12:39.104][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-05 19:12:39.105][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-05 19:12:39.106][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-05 19:12:39.107][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-05 19:12:39.107][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-05 19:12:39.108][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-05 19:12:39.110][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-05 19:12:39.112][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-05 19:12:39.113][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-05 19:12:39.114][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-05 19:12:39.115][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-05 19:12:39.116][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-05 19:12:39.118][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-05 19:12:39.119][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-05 19:12:39.120][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-05 19:12:39.122][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-05 19:12:39.123][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-05 19:12:39.124][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-05 19:12:39.125][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-05 19:12:39.127][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-05 19:12:39.128][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-05 19:12:39.129][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-05 19:12:39.136][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-05 19:12:39.137][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-05 19:12:39.139][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-05 19:12:39.140][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-05 19:12:39.141][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-05 19:12:39.142][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-05 19:12:39.143][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-05 19:12:39.144][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-05 19:12:39.146][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-05 19:12:39.147][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-05 19:12:39.148][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-05 19:12:39.149][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-05 19:12:39.150][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-05 19:12:39.151][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-05 19:12:39.152][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-05 19:12:39.153][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-05 19:12:39.154][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-05 19:12:39.155][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-05 19:12:39.157][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-05 19:12:39.158][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-05 19:12:39.159][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-05 19:12:39.160][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-05 19:12:39.161][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-05 19:12:39.162][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-05 19:12:39.163][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-05 19:12:39.164][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-05 19:12:39.165][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-05 19:12:39.166][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-05 19:12:39.168][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-05 19:12:39.170][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-05 19:12:39.171][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-05 19:12:39.172][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-05 19:12:39.173][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-05 19:12:39.174][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-05 19:12:39.175][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-05 19:12:39.176][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-05 19:12:39.177][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-05 19:12:39.179][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-05 19:12:39.180][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-05 19:12:39.181][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-05 19:12:39.182][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-05 19:12:39.183][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-05 19:12:39.184][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-05 19:12:39.186][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-05 19:12:39.186][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-05 19:12:39.188][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-05 19:12:39.189][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-05 19:12:39.190][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.192][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:39.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:39.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:39.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:39.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:39.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:39.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:39.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:39.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:39.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:39.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:39.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:39.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.212][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[2025-02-05 19:12:39.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:39.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:39.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:39.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:39.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:39.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:39.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:39.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:39.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:39.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:39.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:39.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.233][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[2025-02-05 19:12:39.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:39.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:39.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:39.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:39.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:39.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:39.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:39.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:39.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:39.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:39.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:39.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.255][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[2025-02-05 19:12:39.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:39.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:39.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.260][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[2025-02-05 19:12:39.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:39.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:39.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.265][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[2025-02-05 19:12:39.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:39.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:39.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:39.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:39.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:39.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:39.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:39.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:39.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:39.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:39.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:39.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:39.281][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[2025-02-05 19:12:39.285][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-02-05 19:12:39.287][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-02-05 19:12:39.288][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:39.289][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-05 19:12:39.290][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:39.290][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-05 19:12:39.291][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:39.292][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-05 19:12:39.293][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:39.293][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-02-05 19:12:39.295][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-05 19:12:39.296][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-05 19:12:39.296][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:39.297][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-02-05 19:12:39.298][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-05 19:12:39.299][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-02-05 19:12:39.299][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-02-05 19:12:39.299][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-02-05 19:12:39.299][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-02-05 19:12:39.299][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-02-05 19:12:39.299][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-02-05 19:12:39.299][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-02-05 19:12:39.299][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-02-05 19:12:39.299][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-02-05 19:12:39.299][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-02-05 19:12:39.299][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-02-05 19:12:39.300][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:39.300][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-05 19:12:39.300][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-05 19:12:39.300][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-05 19:12:39.301][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-05 19:12:39.302][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:39.303][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:39.303][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-05 19:12:39.304][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:39.305][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:39.305][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-05 19:12:39.306][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:12:39.306][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-02-05 19:12:39.310][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-05 19:12:39.311][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-05 19:12:39.312][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:39.313][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-02-05 19:12:39.313][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-02-05 19:12:39.314][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-05 19:12:39.315][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-05 19:12:39.317][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-02-05 19:12:39.318][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-05 19:12:39.320][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-05 19:12:39.322][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-05 19:12:39.325][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-02-05 19:12:39.327][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-02-05 19:12:39.329][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-02-05 19:12:39.331][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-02-05 19:12:39.332][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-05 19:12:39.332][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-05 19:12:39.334][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-02-05 19:12:39.335][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-02-05 19:12:39.337][biodb::testThat]
biodb.INFO [2025-02-05 19:12:39.338][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-02-05 19:12:39.338][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:12:39.339][biodb::testThat]
biodb.DEBUG[2025-02-05 19:12:39.342][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-02-05 19:12:39.345][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:12:39.346][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-02-05 19:12:39.347][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:12:39.349][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-02-05 19:12:39.364][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[2025-02-05 19:12:39.369][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:39.370][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:39.372][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-02-05 19:12:39.746][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-02-05 19:12:40.106][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:40.108][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-02-05 19:12:40.113][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-02-05 19:12:40.127][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-05 19:12:40.129][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-02-05 19:12:40.130][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-02-05 19:12:40.131][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-05 19:12:40.132][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:40.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:40.134][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:40.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:40.135][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-02-05 19:12:40.145][biodb::testContext]
biodb.INFO [2025-02-05 19:12:40.146][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-05 19:12:40.147][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-02-05 19:12:40.148][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-05 19:12:40.149][biodb::testContext]
biodb.INFO [2025-02-05 19:12:40.152][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-05 19:12:40.156][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-02-05 19:12:40.181][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-05 19:12:40.182][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-05 19:12:40.183][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-05 19:12:40.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.186][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-05 19:12:40.187][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-05 19:12:40.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.192][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-05 19:12:40.193][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-05 19:12:40.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.195][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.DEBUG[2025-02-05 19:12:40.196][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-05 19:12:40.197][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-05 19:12:40.198][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-05 19:12:40.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.201][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-05 19:12:40.202][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-05 19:12:40.203][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-05 19:12:40.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.207][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-05 19:12:40.218][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-05 19:12:40.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.222][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-05 19:12:40.222][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-05 19:12:40.235][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-05 19:12:40.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.239][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-05 19:12:40.239][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-05 19:12:40.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.245][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-05 19:12:40.246][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-05 19:12:40.247][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-05 19:12:40.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.250][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-05 19:12:40.250][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-05 19:12:40.251][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-05 19:12:40.252][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-05 19:12:40.253][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-05 19:12:40.254][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-05 19:12:40.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.271][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-05 19:12:40.273][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-05 19:12:40.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.278][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-05 19:12:40.279][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-05 19:12:40.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.282][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-05 19:12:40.283][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-05 19:12:40.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.287][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-05 19:12:40.287][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-05 19:12:40.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.291][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-05 19:12:40.292][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-05 19:12:40.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.295][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-05 19:12:40.295][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-05 19:12:40.677][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-05 19:12:40.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.681][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-05 19:12:40.683][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-05 19:12:40.684][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-05 19:12:40.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.688][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-05 19:12:40.690][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:40.691][self$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[2025-02-05 19:12:40.692][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:40.693][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-05 19:12:40.698][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:40.699][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-05 19:12:40.701][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:40.702][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-05 19:12:40.703][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-05 19:12:40.705][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-05 19:12:40.706][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:40.707][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-05 19:12:40.708][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-05 19:12:40.709][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:40.710][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:40.711][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-05 19:12:40.711][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-05 19:12:40.711][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-05 19:12:40.711][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-05 19:12:40.711][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-05 19:12:40.712][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-05 19:12:40.713][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:40.714][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:40.715][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-05 19:12:40.716][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:40.719][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:40.720][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-05 19:12:40.721][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:40.722][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-05 19:12:40.723][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-05 19:12:40.725][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:40.726][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:40.727][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-05 19:12:40.730][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:40.731][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-05 19:12:40.732][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:40.734][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-05 19:12:40.735][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:40.736][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-05 19:12:40.738][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:40.739][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-05 19:12:40.740][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-05 19:12:40.741][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-05 19:12:40.743][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:40.745][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-05 19:12:40.747][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-05 19:12:40.748][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:40.749][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:40.750][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-05 19:12:40.750][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-05 19:12:40.750][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-05 19:12:40.750][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-05 19:12:40.750][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-05 19:12:40.751][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-05 19:12:40.753][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:40.754][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:40.755][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-05 19:12:40.757][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:40.758][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:40.759][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-05 19:12:40.760][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:40.761][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-05 19:12:40.762][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-05 19:12:40.763][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:40.765][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:40.766][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-05 19:12:40.769][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:40.770][self$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[2025-02-05 19:12:40.771][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:40.772][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-05 19:12:40.773][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:40.775][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-05 19:12:40.776][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:40.777][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-05 19:12:40.779][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-05 19:12:40.781][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-05 19:12:40.782][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:40.783][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-05 19:12:40.784][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-05 19:12:40.786][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:40.787][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:40.788][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:40.789][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-05 19:12:40.790][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:40.792][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:40.793][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-05 19:12:40.794][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:40.794][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:40.795][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-05 19:12:40.796][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:40.797][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-05 19:12:40.797][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-05 19:12:40.798][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:40.799][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:40.800][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-05 19:12:40.812][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:40.813][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-05 19:12:40.814][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:40.816][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-05 19:12:40.816][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:40.817][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-05 19:12:40.818][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:40.819][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-05 19:12:40.820][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-05 19:12:40.821][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-05 19:12:40.822][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:40.823][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-05 19:12:40.824][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-05 19:12:40.825][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:40.837][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:40.839][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:40.840][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-05 19:12:40.840][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:40.841][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:40.842][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-05 19:12:40.843][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:40.844][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:40.844][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-05 19:12:40.845][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:40.846][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-05 19:12:40.847][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-05 19:12:40.849][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:40.850][self$setPropertyValue]
biodb.DEBUG[2025-02-05 19:12:40.852][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-05 19:12:40.853][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:40.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:40.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:40.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:40.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:40.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:40.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:40.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:40.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:40.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:40.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:40.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:40.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:40.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:40.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:40.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:40.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:40.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:40.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:40.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:40.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.898][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[2025-02-05 19:12:40.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:40.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:40.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:40.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:40.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:40.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:40.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.912][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[2025-02-05 19:12:40.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:40.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:40.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.917][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[2025-02-05 19:12:40.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:40.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:40.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:40.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:40.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:40.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:40.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:40.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:40.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:40.942][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-05 19:12:40.943][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-05 19:12:40.945][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-05 19:12:40.947][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-05 19:12:40.949][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-05 19:12:40.950][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-05 19:12:40.951][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-05 19:12:40.953][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-05 19:12:40.977][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-05 19:12:40.979][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-05 19:12:40.992][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-05 19:12:40.993][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-05 19:12:40.994][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-05 19:12:40.995][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-05 19:12:40.997][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-05 19:12:40.998][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-05 19:12:40.999][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-05 19:12:41.001][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-05 19:12:41.002][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-05 19:12:41.003][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-05 19:12:41.004][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-05 19:12:41.006][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-05 19:12:41.007][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-05 19:12:41.008][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-05 19:12:41.009][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-05 19:12:41.010][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-05 19:12:41.011][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-05 19:12:41.013][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-05 19:12:41.014][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-05 19:12:41.015][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-05 19:12:41.017][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-05 19:12:41.018][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-05 19:12:41.019][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-05 19:12:41.020][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-05 19:12:41.022][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-05 19:12:41.023][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-05 19:12:41.024][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-05 19:12:41.036][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-05 19:12:41.037][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-05 19:12:41.038][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-05 19:12:41.040][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-05 19:12:41.041][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-05 19:12:41.049][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-05 19:12:41.050][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-05 19:12:41.051][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-05 19:12:41.052][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-05 19:12:41.053][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-05 19:12:41.054][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-05 19:12:41.056][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-05 19:12:41.057][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-05 19:12:41.058][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-05 19:12:41.060][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-05 19:12:41.061][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-05 19:12:41.064][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-05 19:12:41.065][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-05 19:12:41.067][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-05 19:12:41.068][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-05 19:12:41.069][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-05 19:12:41.070][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-05 19:12:41.072][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-05 19:12:41.073][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-05 19:12:41.074][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-05 19:12:41.075][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-05 19:12:41.076][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-05 19:12:41.077][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-05 19:12:41.080][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-05 19:12:41.081][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-05 19:12:41.082][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-05 19:12:41.083][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-05 19:12:41.084][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-05 19:12:41.085][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-05 19:12:41.086][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-05 19:12:41.087][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-05 19:12:41.088][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-05 19:12:41.090][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-05 19:12:41.092][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-05 19:12:41.093][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-05 19:12:41.094][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-05 19:12:41.095][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-05 19:12:41.096][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-05 19:12:41.097][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-05 19:12:41.098][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-05 19:12:41.099][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-05 19:12:41.100][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-05 19:12:41.102][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-05 19:12:41.103][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-05 19:12:41.104][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:41.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:41.105][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:41.106][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[2025-02-05 19:12:41.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:41.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:41.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:41.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:41.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:41.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:41.111][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.DEBUG[2025-02-05 19:12:41.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:41.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:41.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:41.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:41.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:41.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:41.117][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[2025-02-05 19:12:41.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:41.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:41.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:41.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:41.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:41.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:41.121][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[2025-02-05 19:12:41.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:41.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:41.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:41.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:41.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:41.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:41.127][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[2025-02-05 19:12:41.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:41.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:41.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:41.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:41.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:41.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:41.134][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[2025-02-05 19:12:41.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:41.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:41.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:41.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:41.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:41.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:41.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:41.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:41.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:41.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:41.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:41.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:41.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:41.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:41.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:41.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:41.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:41.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:41.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:41.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:41.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:41.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:41.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:41.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:41.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:41.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:41.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:41.158][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[2025-02-05 19:12:41.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:41.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:41.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:41.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:41.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:41.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:41.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:41.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:41.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:41.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:41.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:41.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:41.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:41.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:41.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:41.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:41.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:41.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:41.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:41.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:41.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:41.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:41.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:41.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:41.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:41.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:41.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:41.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:41.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:41.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:41.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:41.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:41.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:41.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:41.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:41.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:41.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:41.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:41.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:41.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:41.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:41.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:41.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:41.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:41.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:41.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:41.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:41.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:41.212][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[2025-02-05 19:12:41.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-05 19:12:41.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:41.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:41.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:41.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:41.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:41.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:41.230][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-02-05 19:12:41.233][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-02-05 19:12:41.235][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:41.236][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-05 19:12:41.237][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:41.238][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-05 19:12:41.239][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:41.240][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-05 19:12:41.240][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:41.241][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-02-05 19:12:41.242][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-05 19:12:41.243][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-05 19:12:41.244][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:41.245][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-02-05 19:12:41.246][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-05 19:12:41.247][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-02-05 19:12:41.247][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-02-05 19:12:41.247][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-02-05 19:12:41.247][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-02-05 19:12:41.247][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-02-05 19:12:41.247][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-02-05 19:12:41.247][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-02-05 19:12:41.247][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-02-05 19:12:41.247][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-02-05 19:12:41.247][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-02-05 19:12:41.247][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-02-05 19:12:41.248][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-05 19:12:41.249][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-05 19:12:41.249][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-05 19:12:41.249][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-05 19:12:41.260][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-05 19:12:41.262][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:41.262][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:41.263][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-05 19:12:41.264][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-05 19:12:41.265][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-05 19:12:41.266][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-05 19:12:41.267][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:12:41.267][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-02-05 19:12:41.268][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-05 19:12:41.269][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-05 19:12:41.270][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-05 19:12:41.270][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-02-05 19:12:41.270][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-02-05 19:12:41.271][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-05 19:12:41.273][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-05 19:12:41.274][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-02-05 19:12:41.275][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-05 19:12:41.276][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-05 19:12:41.278][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-05 19:12:41.281][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-02-05 19:12:41.281][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-02-05 19:12:41.282][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-02-05 19:12:41.284][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-02-05 19:12:41.284][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-05 19:12:41.285][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-05 19:12:41.286][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-02-05 19:12:41.287][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-02-05 19:12:41.288][biodb::testThat]
biodb.INFO [2025-02-05 19:12:41.289][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-02-05 19:12:41.290][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-05 19:12:41.291][biodb::testThat]
biodb.DEBUG[2025-02-05 19:12:41.293][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-02-05 19:12:41.296][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:12:41.297][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-02-05 19:12:41.298][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:12:41.300][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-02-05 19:12:41.314][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-05 19:12:41.317][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-05 19:12:41.319][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-02-05 19:12:41.320][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-05 19:12:41.322][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-02-05 19:12:41.326][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-02-05 19:12:41.327][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-05 19:12:41.328][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-02-05 19:12:41.329][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-05 19:12:41.330][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-05 19:12:41.331][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-05 19:12:41.332][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-05 19:12:41.333][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-05 19:12:41.334][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-05 19:12:41.336][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:41.337][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:41.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:41.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:41.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:41.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:41.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-05 19:12:41.358][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-02-05 19:12:41.361][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-05 19:12:41.361][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-05 19:12:41.362][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-02-05 19:12:41.747][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-02-05 19:12:43.004][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-05 19:12:43.007][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-02-05 19:12:43.033][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-02-05 19:12:43.040][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-02-05 19:12:43.045][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-05 19:12:43.047][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-05 19:12:43.049][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-05 19:12:43.051][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-05 19:12:43.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:43.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:43.063][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:43.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:43.066][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:43.067][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[2025-02-05 19:12:43.086][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:43.087][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:43.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.089][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:43.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:43.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.107][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:43.108][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:43.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.110][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.145][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-05 19:12:43.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-05 19:12:43.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.152][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:43.153][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:43.154][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.155][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.157][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-05 19:12:43.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-05 19:12:43.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.163][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-05 19:12:43.164][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-05 19:12:43.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.168][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.169][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-05 19:12:43.170][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-05 19:12:43.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.172][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.173][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:43.174][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:43.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.177][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.179][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:43.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-05 19:12:43.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.188][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:43.189][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:43.191][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.192][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.194][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-05 19:12:43.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-05 19:12:43.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.201][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:43.204][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:43.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.216][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:43.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-05 19:12:43.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.225][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:43.227][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:43.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.229][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.232][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-05 19:12:43.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-05 19:12:43.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.237][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:43.239][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:43.241][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.242][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.243][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-05 19:12:43.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-05 19:12:43.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.246][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:43.247][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:43.248][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.249][ef$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.250][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-05 19:12:43.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-05 19:12:43.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.265][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:43.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:43.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:43.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:43.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:43.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:43.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-05 19:12:43.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-05 19:12:43.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:43.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:43.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:43.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:43.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:43.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:43.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:43.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:43.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:43.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:43.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-05 19:12:43.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-05 19:12:43.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-05 19:12:43.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-05 19:12:43.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-05 19:12:43.329][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-02-05 19:12:43.334][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-05 19:12:43.335][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-02-05 19:12:43.336][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-02-05 19:12:43.337][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-05 19:12:43.338][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-05 19:12:43.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-05 19:12:43.339][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-05 19:12:43.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-05 19:12:43.341][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-05 19:12:43.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
> 
> proc.time()
   user  system elapsed 
 23.932   1.610  78.067

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

name	user	system	elapsed
ChebiConn	2.668	1.074	5.206
ChebiEntry	0.355	0.018	0.383