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: 2025-02-10 19:44:29 -0500 (Mon, 10 Feb 2025)

EndedAt: 2025-02-10 19:46:42 -0500 (Mon, 10 Feb 2025)

EllapsedTime: 133.0 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 2.716  1.106   5.364
* 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 [2025-02-10 19:45:27.605][biodb::testContext]
biodb.INFO [2025-02-10 19:45:27.610][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-10 19:45:27.612][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-02-10 19:45:27.613][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-10 19:45:27.615][biodb::testContext]
biodb.INFO [2025-02-10 19:45:27.625][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-10 19:45:27.628][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-02-10 19:45:27.638][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 19:45:27.640][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-10 19:45:27.642][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-10 19:45:27.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:27.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:27.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:27.648][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-10 19:45:27.675][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-10 19:45:27.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:27.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:27.680][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[2025-02-10 19:45:27.681][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-10 19:45:27.683][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-10 19:45:27.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:27.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:27.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:27.689][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-10 19:45:27.690][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-10 19:45:27.692][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-10 19:45:27.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:27.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:27.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:27.696][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-10 19:45:27.698][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-10 19:45:27.699][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-10 19:45:27.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:27.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:27.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:27.703][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-10 19:45:27.704][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-10 19:45:27.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:27.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:27.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:27.709][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-10 19:45:27.710][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-10 19:45:27.711][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-10 19:45:27.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:27.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:27.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:27.716][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-10 19:45:27.718][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-10 19:45:27.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:27.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:27.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:27.737][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-10 19:45:27.739][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-10 19:45:27.741][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-10 19:45:27.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:27.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:27.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:27.745][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-10 19:45:27.746][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-10 19:45:27.747][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-10 19:45:27.749][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-10 19:45:27.750][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-10 19:45:27.751][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-10 19:45:27.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:27.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:27.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:27.755][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-10 19:45:27.756][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-10 19:45:27.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:27.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:27.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:27.760][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-10 19:45:27.761][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-10 19:45:27.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:27.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:27.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:27.766][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-10 19:45:27.767][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-10 19:45:27.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:27.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:27.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:27.770][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-10 19:45:27.771][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-10 19:45:27.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:27.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:27.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:27.775][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-10 19:45:27.776][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-10 19:45:27.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:27.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:27.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:27.781][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-10 19:45:27.782][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-10 19:45:27.810][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-10 19:45:27.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:27.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:27.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:27.816][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-10 19:45:27.817][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-10 19:45:27.819][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-10 19:45:27.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:27.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:27.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:27.826][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-10 19:45:27.871][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 19:45:27.893][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-10 19:45:27.911][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 19:45:27.994][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 19:45:27.996][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 19:45:27.998][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 19:45:27.999][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 19:45:28.000][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 19:45:28.001][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-10 19:45:28.002][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 19:45:28.004][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 19:45:28.005][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-10 19:45:28.007][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 19:45:28.008][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:45:28.009][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 19:45:28.011][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 19:45:28.011][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 19:45:28.011][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 19:45:28.011][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-10 19:45:28.011][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-10 19:45:28.012][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 19:45:28.013][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:45:28.015][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:45:28.016][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 19:45:28.017][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:45:28.018][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:45:28.019][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 19:45:28.020][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:45:28.022][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 19:45:28.023][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 19:45:28.024][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 19:45:28.025][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:45:28.026][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-10 19:45:28.029][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 19:45:28.029][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-10 19:45:28.031][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 19:45:28.032][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 19:45:28.033][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 19:45:28.035][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 19:45:28.036][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 19:45:28.037][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 19:45:28.038][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-10 19:45:28.039][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 19:45:28.040][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 19:45:28.041][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-10 19:45:28.043][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 19:45:28.044][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:45:28.045][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 19:45:28.047][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 19:45:28.047][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 19:45:28.047][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 19:45:28.047][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-10 19:45:28.047][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-10 19:45:28.048][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 19:45:28.049][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:45:28.050][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:45:28.052][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 19:45:28.053][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:45:28.054][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:45:28.055][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 19:45:28.056][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:45:28.057][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 19:45:28.058][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 19:45:28.059][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 19:45:28.060][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:45:28.061][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-10 19:45:28.063][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-10 19:45:28.064][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-10 19:45:28.066][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 19:45:28.067][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 19:45:28.068][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 19:45:28.069][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 19:45:28.070][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 19:45:28.071][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 19:45:28.073][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-10 19:45:28.074][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 19:45:28.075][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-10 19:45:28.076][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-10 19:45:28.077][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 19:45:28.078][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:45:28.079][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 19:45:28.081][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:45:28.082][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 19:45:28.083][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:45:28.084][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:45:28.086][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 19:45:28.087][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:45:28.088][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:45:28.089][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 19:45:28.090][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:45:28.091][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 19:45:28.092][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 19:45:28.093][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 19:45:28.094][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:45:28.095][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-10 19:45:28.098][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-10 19:45:28.099][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-10 19:45:28.100][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 19:45:28.101][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 19:45:28.103][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 19:45:28.104][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 19:45:28.105][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 19:45:28.107][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 19:45:28.108][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-10 19:45:28.109][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 19:45:28.111][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-10 19:45:28.112][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-10 19:45:28.113][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 19:45:28.114][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:45:28.116][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 19:45:28.117][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:45:28.118][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 19:45:28.119][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:45:28.129][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:45:28.130][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 19:45:28.132][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:45:28.133][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:45:28.134][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 19:45:28.135][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:45:28.136][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 19:45:28.137][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 19:45:28.138][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 19:45:28.139][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:45:28.144][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 19:45:28.144][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.145][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[2025-02-10 19:45:28.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.151][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.DEBUG[2025-02-10 19:45:28.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.188][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[2025-02-10 19:45:28.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.200][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[2025-02-10 19:45:28.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.205][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[2025-02-10 19:45:28.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.222][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[2025-02-10 19:45:28.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.233][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[2025-02-10 19:45:28.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.240][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-10 19:45:28.245][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-10 19:45:28.247][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-10 19:45:28.249][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-10 19:45:28.251][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-10 19:45:28.252][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-10 19:45:28.254][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-10 19:45:28.257][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-10 19:45:28.259][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-10 19:45:28.261][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-10 19:45:28.262][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-10 19:45:28.264][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-10 19:45:28.266][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-10 19:45:28.267][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-10 19:45:28.269][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-10 19:45:28.270][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-10 19:45:28.272][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-10 19:45:28.274][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-10 19:45:28.276][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-10 19:45:28.277][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-10 19:45:28.279][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-10 19:45:28.281][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-10 19:45:28.282][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-10 19:45:28.284][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-10 19:45:28.286][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-10 19:45:28.288][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-10 19:45:28.290][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-10 19:45:28.292][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-10 19:45:28.294][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-10 19:45:28.296][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-10 19:45:28.297][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-10 19:45:28.299][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-10 19:45:28.301][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-10 19:45:28.302][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-10 19:45:28.304][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-10 19:45:28.305][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-10 19:45:28.307][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-10 19:45:28.309][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-10 19:45:28.310][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-10 19:45:28.312][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-10 19:45:28.313][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-10 19:45:28.315][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-10 19:45:28.317][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-10 19:45:28.319][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-10 19:45:28.320][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-10 19:45:28.322][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-10 19:45:28.323][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-10 19:45:28.324][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-10 19:45:28.326][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-10 19:45:28.327][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-10 19:45:28.329][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-10 19:45:28.331][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-10 19:45:28.333][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-10 19:45:28.335][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-10 19:45:28.336][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-10 19:45:28.338][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-10 19:45:28.340][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-10 19:45:28.342][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-10 19:45:28.343][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-10 19:45:28.345][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-10 19:45:28.347][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-10 19:45:28.349][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-10 19:45:28.350][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-10 19:45:28.352][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-10 19:45:28.354][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-10 19:45:28.356][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-10 19:45:28.357][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-10 19:45:28.359][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-10 19:45:28.361][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-10 19:45:28.362][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-10 19:45:28.364][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-10 19:45:28.365][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-10 19:45:28.366][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-10 19:45:28.368][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-10 19:45:28.369][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-10 19:45:28.371][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-10 19:45:28.373][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-10 19:45:28.375][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-10 19:45:28.377][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-10 19:45:28.378][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-10 19:45:28.380][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-10 19:45:28.382][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-10 19:45:28.391][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-10 19:45:28.398][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-10 19:45:28.401][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-10 19:45:28.405][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 19:45:28.406][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.409][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:28.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:28.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:28.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:28.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:28.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:28.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:28.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:28.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:28.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:28.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:28.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:28.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:28.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:28.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:28.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:28.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.475][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[2025-02-10 19:45:28.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:28.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:28.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:28.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:28.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:28.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:28.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:28.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:28.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:28.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:28.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:28.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:28.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.523][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[2025-02-10 19:45:28.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:28.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:28.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:28.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:28.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:45:28.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:28.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:28.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:28.547][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-02-10 19:45:28.561][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-02-10 19:45:28.564][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 19:45:28.565][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-10 19:45:28.567][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 19:45:28.568][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 19:45:28.569][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 19:45:28.570][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 19:45:28.571][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-10 19:45:28.573][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-02-10 19:45:28.574][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-10 19:45:28.575][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 19:45:28.577][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 19:45:28.578][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-02-10 19:45:28.579][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 19:45:28.581][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-02-10 19:45:28.581][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-02-10 19:45:28.581][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-02-10 19:45:28.581][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-02-10 19:45:28.581][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-02-10 19:45:28.581][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-02-10 19:45:28.581][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-02-10 19:45:28.581][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-02-10 19:45:28.581][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-02-10 19:45:28.581][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-02-10 19:45:28.581][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-02-10 19:45:28.582][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-10 19:45:28.583][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 19:45:28.583][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 19:45:28.583][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 19:45:28.585][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-10 19:45:28.586][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:45:28.587][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:45:28.588][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 19:45:28.589][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:45:28.591][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:45:28.592][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 19:45:28.593][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:45:28.593][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-02-10 19:45:28.594][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 19:45:28.595][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 19:45:28.596][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-10 19:45:28.597][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-02-10 19:45:28.597][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-02-10 19:45:28.604][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-10 19:45:28.607][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-10 19:45:28.609][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-02-10 19:45:28.611][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-10 19:45:28.613][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-10 19:45:28.615][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-10 19:45:28.645][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-02-10 19:45:28.647][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-02-10 19:45:28.653][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-02-10 19:45:28.657][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-02-10 19:45:28.672][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-10 19:45:28.673][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-10 19:45:28.675][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-02-10 19:45:28.676][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-02-10 19:45:28.689][biodb::testThat]
biodb.INFO [2025-02-10 19:45:28.691][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-02-10 19:45:28.692][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:45:28.694][biodb::testThat]
biodb.TRACE[2025-02-10 19:45:28.699][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[2025-02-10 19:45:28.702][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:28.706][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:28.716][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:28.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:28.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:28.738][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:28.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:28.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:28.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:45:28.754][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:28.756][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:28.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.759][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:28.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:28.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.784][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:28.785][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:28.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.787][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.822][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:28.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:28.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.828][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:28.830][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:28.831][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.832][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.834][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:28.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:28.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.840][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:28.841][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:28.842][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.843][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.845][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:28.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:28.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.850][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:28.852][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:28.853][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.854][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.855][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:28.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:28.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.861][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:28.862][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:28.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.865][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.867][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:28.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:28.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.872][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:28.886][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:28.888][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.889][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.891][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:28.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:28.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.897][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:28.898][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:28.899][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.900][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.902][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:28.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:28.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.908][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:28.909][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:28.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.911][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.913][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:28.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:28.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.917][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:28.919][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:28.920][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.922][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.923][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:28.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:28.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.929][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:28.930][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:28.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.932][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.934][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:28.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:28.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.940][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:28.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:28.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:28.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:28.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:28.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:28.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:28.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:28.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:28.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:28.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:29.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:29.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:29.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:29.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:29.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:29.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:29.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:29.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:29.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:29.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:29.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:29.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:29.072][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-02-10 19:45:29.075][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:29.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:29.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.079][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:29.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:29.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.114][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:29.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:29.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.120][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:29.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:29.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:29.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:29.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.130][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:29.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:29.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.135][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-10 19:45:29.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-10 19:45:29.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.140][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-10 19:45:29.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-10 19:45:29.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.145][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-10 19:45:29.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-10 19:45:29.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.150][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-10 19:45:29.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-10 19:45:29.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:29.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:29.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:29.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:29.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:29.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:29.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:29.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:29.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:29.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:29.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:29.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:29.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:29.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:29.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:29.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:29.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.249][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:29.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:29.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.255][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:29.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:29.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:29.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:29.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:29.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:29.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:29.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:29.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:29.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:29.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.290][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:29.292][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:29.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.294][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:29.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:29.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:29.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:29.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:29.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:29.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:29.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:29.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.329][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:29.331][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:29.332][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.334][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.335][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:29.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:29.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.351][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:29.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:29.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.357][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:29.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:29.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.364][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:29.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:29.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.369][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:29.370][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:29.371][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.372][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.373][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:29.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:29.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.391][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:29.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:29.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.397][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:29.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:29.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.402][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:29.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:29.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.407][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:29.409][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:29.410][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.411][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.413][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:29.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:29.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.429][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:29.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:29.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:29.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:29.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:29.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:29.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.444][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:29.453][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:29.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.456][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.457][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:29.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:29.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:29.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:29.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:29.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:29.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:29.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:29.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.490][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:29.491][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:29.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.493][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.495][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:29.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:29.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.512][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:29.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:29.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.517][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:29.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:29.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.522][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:29.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:29.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.527][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:29.528][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:29.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.530][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.531][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:29.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:29.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.548][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-10 19:45:29.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:29.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.554][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-10 19:45:29.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:29.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.559][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-10 19:45:29.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:29.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.564][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-10 19:45:29.565][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:29.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.568][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.569][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-10 19:45:29.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:29.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.586][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:29.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:29.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.591][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:29.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:29.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.595][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:29.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:29.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.600][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:29.601][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:29.603][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.604][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.605][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:29.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:29.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.622][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:29.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:29.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.627][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:29.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:29.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.632][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:29.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:29.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.637][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:29.638][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:29.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.641][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.642][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:29.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:29.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.659][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:29.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:29.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.664][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:29.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:29.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.670][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:29.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:29.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.675][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:29.677][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:29.678][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.679][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.681][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:29.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:29.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.705][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:29.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:29.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.711][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:29.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:29.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.716][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:29.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:29.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.721][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:29.723][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:29.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.725][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.726][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:29.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:29.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.745][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:29.746][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:29.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.749][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.756][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:29.758][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:29.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.761][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.768][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:29.770][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:29.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.772][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.779][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:29.781][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:29.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.783][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.790][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:29.791][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:29.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.794][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.801][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:29.803][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:29.804][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.805][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.813][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:29.814][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:29.815][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.816][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.824][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:29.825][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:29.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.828][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.835][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-10 19:45:29.837][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:29.838][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.840][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.847][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:29.849][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:29.850][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.852][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.859][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:29.860][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:29.862][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.863][ef$get] fields variable is a list.
biodb.INFO [2025-02-10 19:45:29.875][biodb::testThat]
biodb.INFO [2025-02-10 19:45:29.877][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-02-10 19:45:29.879][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:45:29.880][biodb::testThat]
biodb.DEBUG[2025-02-10 19:45:29.900][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-02-10 19:45:29.909][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:45:29.913][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-02-10 19:45:29.915][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:45:29.918][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-02-10 19:45:29.919][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:45:29.960][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:29.962][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:29.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:29.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:29.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:29.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:29.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:29.975][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:29.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:45:29.980][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:29.981][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:29.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.984][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:29.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:29.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:29.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:29.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.014][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:30.015][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:30.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.017][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.020][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:30.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:30.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.025][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:30.027][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:30.028][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.029][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.030][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:30.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:30.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.035][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:30.037][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:30.037][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.039][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.041][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:30.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:30.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.046][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:30.047][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:30.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.049][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.051][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:30.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:30.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.057][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:30.059][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:30.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.061][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.063][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:30.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:30.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.069][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:30.070][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:30.071][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.073][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.074][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:30.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:30.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.080][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:30.081][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:30.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.083][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.085][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:30.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:30.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.090][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:30.092][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:30.093][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.094][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.096][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:30.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:30.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.101][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:30.103][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:30.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.106][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.107][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:30.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:30.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.112][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:30.114][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:30.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.116][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.117][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:30.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:30.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:30.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:30.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.127][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:30.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:30.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:30.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:30.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.136][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:30.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:30.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:30.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:30.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:30.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:30.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:30.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:30.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:30.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:30.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:30.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:30.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:30.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:30.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:30.172][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-02-10 19:45:30.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-02-10 19:45:30.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-02-10 19:45:30.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.185][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-02-10 19:45:30.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-02-10 19:45:30.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-02-10 19:45:30.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-02-10 19:45:30.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-10 19:45:30.207][biodb::testThat]
biodb.INFO [2025-02-10 19:45:30.209][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-02-10 19:45:30.210][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:45:30.212][biodb::testThat]
biodb.TRACE[2025-02-10 19:45:30.216][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:30.218][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:30.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.220][ef$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:30.222][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-02-10 19:45:30.260][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:30.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:30.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.265][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:30.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:30.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:30.271][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:30.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:30.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:30.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:30.279][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-02-10 19:45:30.283][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-02-10 19:45:30.311][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 19:45:30.332][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-02-10 19:45:30.333][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:45:30.336][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-02-10 19:45:30.369][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[2025-02-10 19:45:30.373][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:30.375][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:30.377][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-02-10 19:45:31.349][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-02-10 19:45:31.830][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:31.832][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-02-10 19:45:31.855][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-02-10 19:45:31.858][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-02-10 19:45:31.877][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:31.879][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:31.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:31.881][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:31.882][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:31.884][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:31.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:31.886][ef$get] fields variable is a list.
biodb.INFO [2025-02-10 19:45:31.892][biodb::testThat]
biodb.INFO [2025-02-10 19:45:31.893][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-02-10 19:45:31.894][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:45:31.895][biodb::testThat]
biodb.TRACE[2025-02-10 19:45:31.942][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:31.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:31.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:31.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:31.949][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:31.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:31.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:31.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:31.953][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:31.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:31.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:31.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:32.036][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:45:32.040][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 19:45:32.042][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-10 19:45:32.044][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:45:32.046][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-02-10 19:45:32.074][biodb::testThat]
biodb.INFO [2025-02-10 19:45:32.076][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-02-10 19:45:32.077][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:45:32.079][biodb::testThat]
biodb.TRACE[2025-02-10 19:45:32.118][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:32.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:32.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:32.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:32.125][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:32.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:32.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:32.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:32.131][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:32.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:32.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:32.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:32.136][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:32.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:32.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:32.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:32.142][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:32.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:32.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:32.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:32.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:32.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:32.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:32.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:32.152][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-10 19:45:32.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-10 19:45:32.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:32.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:32.158][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-10 19:45:32.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-10 19:45:32.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:32.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:32.163][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-10 19:45:32.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-10 19:45:32.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:32.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:32.168][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-10 19:45:32.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-10 19:45:32.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:32.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:32.200][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:32.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:32.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:32.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:32.207][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:32.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:32.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:32.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:32.213][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:32.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:32.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:32.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:32.219][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:32.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:32.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:32.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:32.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:32.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:32.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:32.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:32.230][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:32.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:32.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:32.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:32.236][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-10 19:45:32.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-10 19:45:32.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:32.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:32.242][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-10 19:45:32.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-10 19:45:32.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:32.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:32.247][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-10 19:45:32.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-10 19:45:32.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:32.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:32.253][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-10 19:45:32.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-10 19:45:32.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:32.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-10 19:45:32.269][biodb::testThat]
biodb.INFO [2025-02-10 19:45:32.271][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-02-10 19:45:32.272][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:45:32.273][biodb::testThat]
biodb.INFO [2025-02-10 19:45:32.287][biodb::testThat]
biodb.INFO [2025-02-10 19:45:32.288][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-02-10 19:45:32.290][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:45:32.324][biodb::testThat]
biodb.INFO [2025-02-10 19:45:32.346][biodb::testThat]
biodb.INFO [2025-02-10 19:45:32.347][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-02-10 19:45:32.349][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:45:32.350][biodb::testThat]
biodb.DEBUG[2025-02-10 19:45:32.356][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-02-10 19:45:33.235][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-02-10 19:45:34.650][biodb::testThat]
biodb.INFO [2025-02-10 19:45:34.652][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-02-10 19:45:34.653][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:45:34.655][biodb::testThat]
biodb.DEBUG[2025-02-10 19:45:35.064][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[2025-02-10 19:45:35.471][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:35.473][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:35.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:35.476][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:35.478][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:35.479][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:35.481][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:35.482][ef$get] fields variable is a list.
biodb.INFO [2025-02-10 19:45:35.485][biodb::testThat]
biodb.INFO [2025-02-10 19:45:35.486][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-02-10 19:45:35.488][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:45:35.489][biodb::testThat]
biodb.TRACE[2025-02-10 19:45:35.509][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:35.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:35.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:35.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:35.515][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:35.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:35.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:35.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:35.521][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:35.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:35.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:35.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:35.631][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:45:35.653][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 19:45:35.655][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-10 19:45:35.657][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:45:35.660][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-02-10 19:45:35.747][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:45:35.751][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 19:45:35.754][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-10 19:45:35.756][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:45:35.758][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-02-10 19:45:35.780][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-10 19:45:35.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-10 19:45:35.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:35.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:35.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:35.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:35.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:35.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:35.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:35.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:35.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:35.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:35.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:35.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:35.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:35.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:35.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:35.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:35.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:35.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:35.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:35.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:35.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:35.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:35.840][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:45:35.861][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:35.881][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:35.902][private$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[2025-02-10 19:45:36.252][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[2025-02-10 19:45:36.601][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:36.604][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-02-10 19:45:36.610][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-02-10 19:45:36.614][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:36.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:36.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:36.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:36.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:36.628][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:36.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:36.631][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-02-10 19:45:36.697][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:45:36.712][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-02-10 19:45:36.714][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:45:36.715][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:45:36.717][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:45:36.719][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:45:36.720][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:45:36.721][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:45:36.725][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:36.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:36.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:36.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:36.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:36.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:36.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:36.742][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-02-10 19:45:36.746][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:36.748][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:36.750][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-02-10 19:45:37.124][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-02-10 19:45:37.482][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:37.485][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-02-10 19:45:37.490][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-02-10 19:45:37.494][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-02-10 19:45:37.496][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:45:37.498][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:37.499][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:37.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:37.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:37.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:37.512][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:37.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:37.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:37.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:45:37.519][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:37.520][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:37.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.524][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:37.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:37.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.531][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:37.532][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:37.534][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.535][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.537][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:37.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:37.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.543][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:37.544][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:37.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.546][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.548][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:37.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:37.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.553][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:37.554][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:37.555][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.557][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.558][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:37.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:37.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.564][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:37.565][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:37.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.568][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.570][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:37.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:37.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.575][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:37.577][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:37.578][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.580][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.581][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:37.583][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:37.584][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.585][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.587][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:37.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:37.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.592][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:37.593][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:37.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.596][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.597][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:37.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:37.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.603][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:37.604][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:37.605][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.606][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.608][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:37.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:37.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.614][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:37.615][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:37.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.618][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.619][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:37.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:37.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.637][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:37.638][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:37.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.641][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.643][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:37.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:37.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:37.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:37.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:37.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:37.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:37.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:37.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:37.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:37.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:37.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:37.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:37.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:37.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:37.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:37.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:37.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:37.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:37.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:37.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:37.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:37.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:37.702][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-02-10 19:45:37.716][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:37.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:37.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.722][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:37.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:37.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:37.728][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:37.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:37.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:37.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:37.734][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[2025-02-10 19:45:37.738][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:37.740][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:37.742][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-02-10 19:45:38.100][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-02-10 19:45:38.457][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:38.460][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-02-10 19:45:38.466][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-02-10 19:45:38.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:38.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:38.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:38.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:38.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:38.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:38.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:45:38.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:38.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:38.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:38.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:38.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:38.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:38.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:38.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:38.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:38.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:38.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:38.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:38.535][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:38.536][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:38.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:38.545][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:38.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:38.548][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:38.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:38.551][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-02-10 19:45:38.553][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:45:38.555][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-02-10 19:45:38.557][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:45:38.558][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:45:38.560][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:45:38.561][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:45:38.562][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:45:38.564][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:45:38.583][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:38.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:38.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:38.594][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:38.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:38.596][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:38.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:38.598][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-02-10 19:45:38.602][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:38.603][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:38.605][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-02-10 19:45:39.008][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-02-10 19:45:39.359][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:39.363][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-02-10 19:45:39.368][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-02-10 19:45:39.372][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-02-10 19:45:39.375][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:45:39.377][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:39.378][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:39.381][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:39.382][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:39.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:39.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:39.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:39.395][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:39.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:45:39.400][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:39.402][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:39.403][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.404][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:39.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:39.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.412][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:39.414][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:39.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.417][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.418][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:39.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:39.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.425][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:39.426][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:39.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.429][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.431][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:39.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:39.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.436][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:39.438][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:39.439][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.440][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.442][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:39.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:39.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.481][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:39.482][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:39.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.485][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.487][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:39.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:39.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.503][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:39.505][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:39.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.508][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.510][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:39.511][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:39.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.514][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.515][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:39.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:39.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.521][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:39.522][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:39.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.525][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:39.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:39.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.532][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:39.533][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:39.535][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.536][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.538][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:39.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:39.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.543][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:39.545][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:39.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.548][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.550][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:39.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:39.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.554][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:39.555][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:39.557][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.558][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.560][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:39.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:39.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:39.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:39.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:39.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:39.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:39.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:39.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:39.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:39.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:39.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:39.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:39.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:39.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:39.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:39.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:39.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:39.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:39.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:39.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:39.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:39.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:39.619][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-02-10 19:45:39.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:39.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:39.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:39.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:39.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.632][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:39.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:39.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:39.668][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:45:39.673][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 19:45:39.675][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-10 19:45:39.677][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:45:39.679][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-02-10 19:45:39.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:39.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:39.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:39.701][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:39.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:39.704][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:39.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:45:39.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:39.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:39.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.712][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:39.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:39.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:39.718][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:39.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:39.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:39.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:39.723][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:39.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:39.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:39.733][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:39.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:39.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:39.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:39.739][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-02-10 19:45:39.740][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:45:39.742][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-02-10 19:45:39.744][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:45:39.746][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:45:39.747][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:45:39.748][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:45:39.750][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:45:39.751][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:45:39.755][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:39.756][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:39.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:39.765][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:39.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:39.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:39.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:39.771][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-02-10 19:45:39.775][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:39.776][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:39.778][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-02-10 19:45:40.148][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-02-10 19:45:40.499][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:40.503][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-02-10 19:45:40.507][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-02-10 19:45:40.511][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-02-10 19:45:40.514][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:45:40.515][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:40.517][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:40.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:40.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:40.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:40.528][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:40.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:40.531][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:40.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:45:40.535][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:40.537][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:40.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.539][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:40.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:40.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.546][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:40.548][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:40.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.551][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.552][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:40.554][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:40.555][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.556][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.558][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:40.560][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:40.562][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.563][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.564][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:40.566][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:40.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.568][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.570][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:40.572][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:40.573][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.574][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.576][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:40.577][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:40.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.580][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.582][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:40.583][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:40.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.586][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.587][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:40.589][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:40.590][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.598][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.605][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:40.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:40.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.612][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:40.613][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:40.615][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.616][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.618][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:40.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:40.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.623][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:40.624][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:40.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.627][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.629][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:40.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:40.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:40.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:40.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:40.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:40.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.645][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:40.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:40.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:40.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:40.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:40.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:40.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:40.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:40.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:40.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:40.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:40.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:40.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:40.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:40.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:40.683][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-02-10 19:45:40.684][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:40.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:40.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.689][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:40.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:40.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:40.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:40.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:40.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:40.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:40.705][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:40.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:40.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:40.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:40.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:40.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:40.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:40.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:40.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:40.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:40.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:40.727][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-02-10 19:45:40.728][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:45:40.730][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-02-10 19:45:40.732][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:45:40.733][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:45:40.735][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:45:40.736][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:45:40.738][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:45:40.739][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:45:40.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:40.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:40.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:40.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:40.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:40.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:40.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:40.758][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-02-10 19:45:40.762][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:40.763][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:40.765][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-02-10 19:45:41.141][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-02-10 19:45:41.507][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:41.510][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-02-10 19:45:41.515][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-02-10 19:45:41.531][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-02-10 19:45:41.533][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:45:41.535][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:41.537][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:41.539][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:41.540][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:41.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:41.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:41.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:41.552][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:41.553][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.TRACE[2025-02-10 19:45:41.556][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:41.558][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:41.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.560][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:41.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:41.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.567][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:41.569][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:41.570][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.571][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.573][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:41.574][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:41.576][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.577][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.579][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:41.581][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:41.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.583][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.585][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:41.586][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:41.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.589][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.591][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:41.592][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:41.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.595][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.596][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:41.598][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:41.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.600][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.602][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:41.603][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:41.605][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.606][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.608][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:41.609][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:41.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.612][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.615][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:41.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:41.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.621][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:41.623][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:41.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.625][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.627][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:41.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:41.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.632][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:41.634][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:41.635][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.635][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:41.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:41.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:41.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:41.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:41.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:41.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:41.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:41.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:41.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:41.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:41.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:41.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:41.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:41.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:41.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:41.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:41.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:41.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:41.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:41.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:41.689][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-02-10 19:45:41.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:41.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:41.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.696][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:41.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:41.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:41.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:41.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:41.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:41.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:41.719][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:41.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:41.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:41.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:41.724][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:41.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:41.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:41.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:41.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:41.737][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:41.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:41.740][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-02-10 19:45:41.742][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:45:41.744][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-02-10 19:45:41.745][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:45:41.747][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:45:41.749][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:45:41.750][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:45:41.751][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:45:41.752][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:45:41.755][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:41.756][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:41.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:41.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:41.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:41.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:41.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:41.771][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-02-10 19:45:41.775][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:41.776][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:41.778][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-02-10 19:45:42.149][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-02-10 19:45:42.506][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:42.509][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-02-10 19:45:42.514][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-02-10 19:45:42.517][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-02-10 19:45:42.520][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:45:42.522][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:42.524][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:42.526][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:42.527][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:42.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:42.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:42.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:42.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:42.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:45:42.542][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:42.544][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:42.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.546][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:42.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:42.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.553][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:42.555][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:42.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.557][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.558][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:42.560][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:42.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.562][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.564][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:42.565][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:42.566][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.568][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.569][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:42.571][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:42.572][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.573][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.575][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:42.576][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:42.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.578][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.580][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:42.581][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:42.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.583][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.585][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:42.586][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:42.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.588][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.590][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:42.591][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:42.592][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.594][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.596][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:42.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:42.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.603][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:42.605][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:42.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.615][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.621][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:42.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:42.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.627][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:42.628][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:42.629][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.630][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:42.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:42.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:42.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:42.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:42.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:42.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:42.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:42.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:42.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:42.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:42.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:42.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:42.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:42.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:42.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:42.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:42.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:42.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:42.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:42.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:42.682][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-02-10 19:45:42.684][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:42.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:42.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.689][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:42.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:42.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.694][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:42.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:42.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.699][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:42.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:42.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:42.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:42.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:42.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:42.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:42.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:42.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:42.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:42.718][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:42.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:42.721][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:42.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:42.723][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-02-10 19:45:42.725][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:45:42.727][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-02-10 19:45:42.728][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:45:42.730][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:45:42.731][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:45:42.732][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:45:42.733][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:45:42.734][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:45:42.737][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:42.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:42.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:42.747][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:42.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:42.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:42.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:42.753][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-02-10 19:45:42.756][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:42.757][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:42.759][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-02-10 19:45:43.161][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-02-10 19:45:43.532][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:43.535][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-02-10 19:45:43.540][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-02-10 19:45:43.544][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-02-10 19:45:43.547][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:45:43.548][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:43.550][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:43.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:43.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:43.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:43.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:43.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:43.601][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:43.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:45:43.606][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:43.608][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:43.609][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.610][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:43.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:43.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.616][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:43.618][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:43.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.620][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.622][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:43.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:43.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.627][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:43.629][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:43.630][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.631][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.633][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:43.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:43.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.638][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:43.640][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:43.641][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.642][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.643][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:43.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:43.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.647][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:43.649][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:43.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.651][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.653][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:43.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:43.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.657][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:43.658][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:43.659][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.660][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.662][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:43.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:43.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.667][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:43.668][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:43.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.671][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.672][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:43.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:43.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.677][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:43.679][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:43.680][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.681][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:43.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:43.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.686][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:43.687][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:43.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.689][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.691][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:43.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:43.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.697][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:43.698][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:43.699][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.700][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.702][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:43.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:43.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.708][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:43.709][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:43.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.711][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.712][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:43.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:43.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:43.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:43.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:43.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:43.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:43.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:43.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:43.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:43.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:43.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:43.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:43.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:43.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:43.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:43.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:43.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:43.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:43.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:43.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:43.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:43.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:43.773][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-02-10 19:45:43.774][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:43.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:43.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:43.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:43.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:43.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:43.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:43.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:43.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:43.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:43.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:43.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:43.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:43.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:43.802][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:43.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:43.805][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-02-10 19:45:43.806][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:45:43.808][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-02-10 19:45:43.810][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:45:43.812][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:45:43.813][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:45:43.815][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:45:43.816][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:45:43.817][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:45:43.819][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:43.821][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:43.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:43.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:43.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:43.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:43.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:43.834][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-02-10 19:45:43.837][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:43.838][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:43.840][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-02-10 19:45:44.247][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-02-10 19:45:44.603][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:44.606][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-02-10 19:45:44.612][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-02-10 19:45:44.616][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-02-10 19:45:44.618][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:45:44.620][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:44.622][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:44.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:44.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:44.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:44.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:44.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:44.637][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:44.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:45:44.641][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:44.642][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:44.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.645][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:44.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:44.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.652][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:44.653][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:44.654][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.656][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.657][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:44.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:44.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.662][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:44.664][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:44.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.666][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.668][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:44.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:44.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.673][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:44.674][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:44.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.676][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.677][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:44.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:44.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.682][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:44.684][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:44.685][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.686][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.700][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:44.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:44.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.706][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:44.708][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:44.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.711][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.712][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:44.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:44.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.718][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:44.719][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:44.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.721][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.723][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:44.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:44.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.728][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:44.729][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:44.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.731][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.733][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:44.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:44.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.738][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:44.740][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:44.741][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.742][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.744][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:44.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:44.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.750][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:44.751][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:44.753][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.754][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.755][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:44.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:44.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.760][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:44.761][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:44.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.764][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.765][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:44.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:44.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:44.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:44.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.775][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:44.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:44.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:44.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:44.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:44.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:44.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:44.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:44.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:44.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:44.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:44.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:44.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:44.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:44.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:44.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:44.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:44.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:44.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:44.821][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-02-10 19:45:44.822][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:44.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:44.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:44.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:44.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:44.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:44.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:44.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:44.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:44.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:44.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:44.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:44.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:44.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:44.850][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:44.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:44.853][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-02-10 19:45:44.854][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:45:44.856][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-02-10 19:45:44.857][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:45:44.859][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:45:44.860][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:45:44.862][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:45:44.863][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:45:44.864][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:45:44.876][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:44.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:44.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:44.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:44.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:44.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:44.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:44.893][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-02-10 19:45:44.897][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:44.898][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:44.899][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-02-10 19:45:45.280][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-02-10 19:45:45.646][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:45.648][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-02-10 19:45:45.652][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-02-10 19:45:45.656][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-02-10 19:45:45.659][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:45:45.660][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:45.662][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:45.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:45.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:45.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:45.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:45.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:45.677][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:45.679][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[2025-02-10 19:45:45.682][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:45.684][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:45.685][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.686][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:45.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:45.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.694][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:45.695][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:45.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.698][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.699][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:45.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:45.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.705][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:45.706][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:45.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.708][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.710][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:45.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:45.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.715][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:45.717][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:45.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.719][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.721][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:45.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:45.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.726][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:45.727][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:45.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.730][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.732][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:45.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:45.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.737][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:45.739][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:45.740][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.742][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.743][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:45.745][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:45.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.747][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.749][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:45.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:45.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.753][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:45.755][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:45.756][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.757][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:45.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:45.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.765][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:45.766][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:45.767][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.768][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.771][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:45.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:45.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.775][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:45.777][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:45.778][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.779][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.781][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:45.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:45.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.787][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:45.788][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:45.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.790][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.791][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:45.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:45.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:45.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:45.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:45.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:45.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:45.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:45.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:45.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:45.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:45.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:45.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:45.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:45.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:45.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:45.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:45.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:45.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:45.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:45.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:45.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:45.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:45.860][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-02-10 19:45:45.861][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:45.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:45.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.867][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:45.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:45.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:45.872][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:45.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:45.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:45.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:45.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:45.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:45.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:45.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:45.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:45.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:45.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:45.893][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-02-10 19:45:45.895][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:45:45.897][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-02-10 19:45:45.899][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:45:45.900][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:45:45.902][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:45:45.903][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:45:45.904][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:45:45.905][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:45:45.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:45.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:45.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:45.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:45.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:45.920][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:45.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:45.923][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-02-10 19:45:45.926][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:45.928][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:45.930][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-02-10 19:45:46.304][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-02-10 19:45:46.669][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:46.672][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-02-10 19:45:46.677][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-02-10 19:45:46.681][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-02-10 19:45:46.683][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:45:46.685][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:46.687][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:46.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:46.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:46.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:46.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:46.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:46.703][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:46.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:45:46.707][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:46.708][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:46.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.711][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:46.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:46.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.731][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:46.733][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:46.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.735][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.737][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:46.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:46.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.742][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:46.743][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:46.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.745][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.747][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:46.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:46.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.752][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:46.754][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:46.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.756][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.758][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:46.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:46.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.763][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:46.764][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:46.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.766][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.767][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:46.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:46.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.772][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:46.773][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:46.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.775][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.776][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:46.778][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:46.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.780][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.782][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:46.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:46.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.787][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:46.788][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:46.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.791][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:46.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:46.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.797][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:46.798][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:46.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.800][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.802][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:46.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:46.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.807][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:46.809][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:46.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.811][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.813][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:46.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:46.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.817][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:46.819][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:46.820][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.821][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.823][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:46.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:46.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.828][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:46.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:46.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.833][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:46.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:46.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:46.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:46.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:46.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:46.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:46.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:46.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:46.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:46.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:46.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:46.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:46.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:46.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:46.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:46.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:46.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:46.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:46.878][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-02-10 19:45:46.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:46.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:46.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:46.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:46.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:46.902][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:46.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:46.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:46.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:46.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:46.909][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:46.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:46.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:46.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:46.922][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:46.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:46.925][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-02-10 19:45:46.926][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:45:46.929][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-02-10 19:45:46.931][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:45:46.932][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:45:46.934][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:45:46.935][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:45:46.936][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:45:46.937][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:45:46.941][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:46.942][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:46.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:46.951][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:46.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:46.954][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:46.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:46.957][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-02-10 19:45:46.961][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:46.963][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:46.964][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-02-10 19:45:47.342][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-02-10 19:45:47.705][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:47.708][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-02-10 19:45:47.713][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-02-10 19:45:47.717][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-02-10 19:45:47.719][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:45:47.720][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:47.721][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:47.723][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:47.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:47.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:47.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:47.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:47.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:47.736][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[2025-02-10 19:45:47.738][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:47.739][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:47.741][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.742][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:47.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:47.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.748][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:47.749][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:47.750][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.751][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.753][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:47.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:47.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.758][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:47.759][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:47.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.761][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.763][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:47.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:47.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.768][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:47.770][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:47.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.772][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.773][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:47.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:47.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.778][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:47.779][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:47.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.781][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.783][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:47.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:47.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.788][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:47.789][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:47.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.791][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.792][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:47.794][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:47.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.796][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.797][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:47.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:47.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.802][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:47.804][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:47.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.816][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:47.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:47.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.824][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:47.825][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:47.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.827][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.829][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:47.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:47.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.834][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:47.836][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:47.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.838][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.839][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:47.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:47.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.844][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:47.845][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:47.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.848][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.850][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:47.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:47.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:47.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:47.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:47.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:47.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:47.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:47.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:47.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:47.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:47.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:47.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:47.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:47.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:47.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:47.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:47.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:47.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:47.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:47.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:47.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:47.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:47.902][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-02-10 19:45:47.903][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:47.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:47.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:47.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:47.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:47.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:47.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:47.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:47.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:47.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:47.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:47.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:47.925][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:47.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:47.927][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:47.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:47.929][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-02-10 19:45:47.931][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:45:47.932][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-02-10 19:45:47.934][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:45:47.936][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:45:47.937][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:45:47.939][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:45:47.940][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:45:47.940][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:45:47.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:47.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:47.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:47.953][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:47.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:47.956][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:47.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:47.958][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-02-10 19:45:47.962][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:47.963][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:47.964][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-02-10 19:45:48.337][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-02-10 19:45:48.691][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:48.694][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-02-10 19:45:48.711][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-02-10 19:45:48.715][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-02-10 19:45:48.717][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:45:48.719][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:48.720][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:48.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:48.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:48.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:48.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:48.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:48.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:48.736][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[2025-02-10 19:45:48.739][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:48.741][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:48.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.743][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:48.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:48.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.750][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:48.751][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:48.752][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.753][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.755][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:48.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:48.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.760][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:48.761][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:48.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.764][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.765][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:48.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:48.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.770][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:48.772][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:48.773][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.774][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.776][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:48.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:48.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.781][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:48.782][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:48.783][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.784][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.786][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:48.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:48.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.791][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:48.793][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:48.794][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.795][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.797][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:48.799][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:48.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.801][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.803][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:48.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:48.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.808][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:48.809][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:48.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.811][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:48.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:48.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.817][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:48.818][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:48.819][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.820][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.821][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:48.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:48.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.826][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:48.827][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:48.828][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.829][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.830][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:48.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:48.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.835][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:48.836][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:48.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.838][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.839][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:48.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:48.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.844][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:48.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:48.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:48.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:48.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:48.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:48.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:48.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:48.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:48.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:48.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:48.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:48.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:48.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:48.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:48.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:48.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:48.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:48.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:48.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:48.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:48.902][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-02-10 19:45:48.904][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:48.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:48.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.909][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:48.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:48.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:48.914][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:48.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:48.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:48.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:48.919][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:48.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:48.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:48.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:48.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:48.931][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:48.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:48.934][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-02-10 19:45:48.935][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:45:48.937][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-02-10 19:45:48.939][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:45:48.940][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:45:48.941][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:45:48.942][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:45:48.943][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:45:48.944][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:45:48.947][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:48.948][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:48.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:48.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:48.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:48.959][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:48.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:48.961][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-02-10 19:45:48.965][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:48.966][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:48.968][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-02-10 19:45:49.353][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-02-10 19:45:49.720][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:49.724][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-02-10 19:45:49.728][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-02-10 19:45:49.732][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-02-10 19:45:49.734][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:45:49.736][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:49.738][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:49.740][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:49.741][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:49.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:49.748][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:49.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:49.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:49.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:45:49.755][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:49.756][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:49.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.759][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:49.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:49.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.766][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:49.767][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:49.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.769][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.771][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:49.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:49.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.777][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:49.778][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:49.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.780][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.782][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:49.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:49.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.787][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:49.788][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:49.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.797][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.802][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:49.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:49.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.806][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:49.807][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:49.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.809][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.811][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:49.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:49.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.816][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:49.817][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:49.818][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.820][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.821][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:49.823][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:49.824][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.825][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.827][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:49.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:49.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.832][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:49.834][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:49.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.836][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:49.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:49.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.843][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:49.844][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:49.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.846][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.848][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:49.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:49.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.852][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:49.853][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:49.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.855][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.856][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:49.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:49.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.861][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:49.862][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:49.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.865][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.866][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:49.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:49.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:49.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:49.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:49.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:49.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:49.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:49.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:49.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:49.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:49.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:49.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:49.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:49.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:49.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:49.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:49.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:49.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:49.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:49.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:49.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:49.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:49.920][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-02-10 19:45:49.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:49.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:49.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:49.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:49.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:49.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:49.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:49.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:49.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:49.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:49.938][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:49.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:49.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:49.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:49.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:49.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:49.951][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-02-10 19:45:49.953][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:45:49.955][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-02-10 19:45:49.964][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:45:49.966][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:45:49.968][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:45:49.969][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:45:49.971][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:45:49.972][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:45:49.974][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:49.975][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:49.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:49.983][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:49.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:49.986][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:49.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:49.989][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-02-10 19:45:49.993][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:49.994][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:49.995][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-02-10 19:45:50.354][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-02-10 19:45:50.704][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:50.707][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-02-10 19:45:50.712][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-02-10 19:45:50.715][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-02-10 19:45:50.717][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:45:50.719][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:50.721][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:50.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:50.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:50.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:50.731][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:50.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:50.733][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:50.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:45:50.737][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:50.738][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:50.739][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.741][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:50.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:50.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.746][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:50.747][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:50.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.750][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.751][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:50.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:50.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.756][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:50.757][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:50.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.759][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.761][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:50.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:50.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.765][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:50.766][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:50.767][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.768][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.770][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:50.771][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:50.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.773][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.774][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:50.776][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:50.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.778][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.780][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:50.781][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:50.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.783][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.785][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:50.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:50.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.791][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:50.792][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:50.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.794][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:50.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:50.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.800][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:50.801][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:50.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.804][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.806][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:50.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:50.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.810][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:50.811][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:50.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.813][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.814][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:50.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:50.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.819][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:50.820][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:50.821][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.822][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:50.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:50.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:50.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:50.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:50.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:50.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.848][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:50.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:50.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:50.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:50.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:50.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:50.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:50.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:50.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:50.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:50.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:50.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:50.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:50.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:50.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:50.880][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-02-10 19:45:50.882][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:50.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:50.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:50.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:50.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:50.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:50.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:50.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:50.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:50.895][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:50.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:50.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:50.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:50.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:50.906][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:50.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:50.908][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-02-10 19:45:50.909][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:45:50.911][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-02-10 19:45:50.912][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:45:50.913][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:45:50.914][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:45:50.915][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:45:50.916][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:45:50.917][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:45:50.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:50.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:50.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:50.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:50.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:50.932][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:50.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:50.934][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-02-10 19:45:50.937][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:50.938][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:50.940][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-02-10 19:45:51.309][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-02-10 19:45:51.661][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:51.664][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-02-10 19:45:51.668][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-02-10 19:45:51.672][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-02-10 19:45:51.674][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:45:51.676][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:51.678][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:51.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:51.680][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:51.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:51.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:51.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:51.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:51.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:45:51.695][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:51.696][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:51.697][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.698][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:51.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:51.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.704][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:51.714][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:51.716][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.718][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.720][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:51.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:51.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.725][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:51.727][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:51.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.729][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.730][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:51.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:51.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.735][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:51.736][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:51.737][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.738][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.740][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:51.741][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:51.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.743][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.744][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:51.745][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:51.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.747][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.749][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:51.750][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:51.752][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.753][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.754][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:51.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:51.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.759][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:51.760][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:51.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.762][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:51.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:51.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.768][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:51.769][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:51.770][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.771][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.773][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:51.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:51.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.778][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:51.779][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:51.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.781][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.783][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:51.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:51.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.788][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:51.790][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:51.791][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.792][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:51.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:51.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:51.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:51.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:51.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:51.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:51.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:51.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:51.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:51.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:51.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:51.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:51.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:51.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:51.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:51.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:51.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:51.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:51.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:51.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:51.838][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-02-10 19:45:51.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:51.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:51.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.844][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:51.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:51.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:51.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:51.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:51.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:51.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:51.853][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:51.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:51.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:51.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:51.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:51.871][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:51.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:51.873][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-02-10 19:45:51.875][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:45:51.876][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-02-10 19:45:51.877][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:45:51.878][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:45:51.880][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:45:51.881][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:45:51.882][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:45:51.883][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:45:51.886][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:51.886][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:51.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:51.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:51.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:51.897][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:51.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:51.899][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-02-10 19:45:51.902][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:51.904][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:51.905][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-02-10 19:45:52.267][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-02-10 19:45:52.634][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:52.636][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-02-10 19:45:52.641][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-02-10 19:45:52.644][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-02-10 19:45:52.646][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:45:52.648][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:52.650][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:52.652][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:52.653][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:52.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:52.662][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:52.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:52.664][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:52.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:45:52.667][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:52.669][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:52.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.671][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:52.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:52.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.678][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:52.679][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:52.680][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.681][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.683][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:52.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:52.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.688][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:52.689][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:52.690][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.691][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.693][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:52.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:52.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.697][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:52.698][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:52.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.701][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.702][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:52.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:52.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.708][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:52.709][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:52.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.712][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.713][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:52.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:52.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.718][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:52.719][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:52.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.721][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.722][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:52.724][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:52.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.726][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.727][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:52.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:52.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.732][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:52.733][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:52.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.735][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:52.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:52.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.741][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:52.742][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:52.743][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.744][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.746][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:52.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:52.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.764][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:52.765][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:52.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.767][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.769][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:52.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:52.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.773][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:52.775][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:52.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.776][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.778][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:52.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:52.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:52.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:52.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:52.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:52.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:52.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:52.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:52.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:52.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:52.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:52.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:52.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:52.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:52.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:52.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:52.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:52.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:52.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:52.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:52.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:52.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:52.828][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-02-10 19:45:52.829][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:52.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:52.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:52.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:52.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:52.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:52.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:52.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:52.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:52.844][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:52.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:52.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:52.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:52.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:52.856][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:52.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:52.859][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-02-10 19:45:52.860][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:45:52.862][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-02-10 19:45:52.864][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:45:52.865][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:45:52.866][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:45:52.867][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:45:52.868][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:45:52.869][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:45:52.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:52.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:52.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:52.883][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:52.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:52.886][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:52.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:52.889][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-02-10 19:45:52.892][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:52.893][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:52.895][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-02-10 19:45:53.261][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-02-10 19:45:53.614][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:53.618][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-02-10 19:45:53.622][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-02-10 19:45:53.625][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-02-10 19:45:53.626][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:45:53.628][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:53.630][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:53.632][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:53.644][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:53.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:53.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:53.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:53.656][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:53.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:45:53.661][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:53.662][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:53.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.665][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:53.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:53.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.671][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:53.672][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:53.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.674][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.675][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:53.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:53.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.680][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:53.681][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:53.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.683][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.685][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:53.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:53.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.689][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:53.690][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:53.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.692][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.694][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:53.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:53.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.698][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:53.699][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:53.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.701][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.702][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:53.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:53.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.707][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:53.708][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:53.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.710][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.712][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:53.713][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:53.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.715][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.716][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:53.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:53.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.722][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:53.723][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:53.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.725][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:53.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:53.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.730][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:53.731][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:53.732][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.733][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.734][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:53.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:53.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.739][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:53.741][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:53.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.743][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.744][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:53.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:53.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.749][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:53.750][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:53.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.752][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.753][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:53.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:53.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:53.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:53.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:53.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:53.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:53.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:53.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:53.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:53.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:53.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:53.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:53.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:53.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:53.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:53.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:53.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:53.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:53.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:53.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:53.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:53.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:53.806][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-02-10 19:45:53.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:53.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:53.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:53.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:53.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:53.817][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:53.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:53.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:53.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:53.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:53.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:53.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:53.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:53.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:53.831][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:53.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:53.834][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-02-10 19:45:53.835][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:45:53.837][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-02-10 19:45:53.838][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:45:53.840][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:45:53.841][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:45:53.843][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:45:53.844][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:45:53.844][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:45:53.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:53.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:53.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:53.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:53.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:53.858][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:53.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:53.860][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-02-10 19:45:53.864][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:53.865][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:53.866][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-02-10 19:45:54.243][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-02-10 19:45:54.615][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:54.617][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-02-10 19:45:54.621][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-02-10 19:45:54.625][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-02-10 19:45:54.627][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:45:54.628][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:54.629][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:54.632][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:54.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:54.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:54.640][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:54.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:54.642][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:54.644][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.TRACE[2025-02-10 19:45:54.646][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:54.648][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:54.649][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.650][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:54.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:54.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.656][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:54.657][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:54.658][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.660][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.661][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:54.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:54.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.665][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:54.666][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:54.667][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.668][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.670][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:54.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:54.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.675][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:54.676][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:54.678][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.679][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.680][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:54.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:54.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.685][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:54.687][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:54.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.702][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.706][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:54.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:54.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.712][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:54.713][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:54.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.715][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.716][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:54.717][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:54.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.719][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.720][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:54.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:54.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.724][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:54.725][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:54.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.727][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:54.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:54.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.733][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:54.734][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:54.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.736][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.737][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:54.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:54.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.742][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:54.743][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:54.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.745][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.747][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:54.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:54.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.751][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:54.752][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:54.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.755][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.756][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:54.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:54.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.762][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:54.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:54.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:54.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:54.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:54.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:54.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.775][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:54.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:54.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:54.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:54.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:54.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:54.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:54.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:54.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:54.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:54.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:54.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:54.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:54.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:54.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:54.810][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-02-10 19:45:54.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:54.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:54.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:54.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:54.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:54.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:54.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:54.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:54.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:54.826][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:54.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:54.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:54.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:54.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:54.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:54.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:54.841][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-02-10 19:45:54.842][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:45:54.844][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-02-10 19:45:54.846][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:45:54.847][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:45:54.849][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:45:54.850][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:45:54.851][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:45:54.858][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:45:54.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:54.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:54.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:54.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:54.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:54.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:54.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:54.877][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-02-10 19:45:54.881][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:54.882][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:54.883][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-02-10 19:45:55.250][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-02-10 19:45:55.605][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:55.609][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-02-10 19:45:55.613][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-02-10 19:45:55.618][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-02-10 19:45:55.620][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:45:55.622][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:55.623][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:55.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:55.627][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:55.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:55.636][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:55.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:55.638][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:55.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:45:55.643][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:55.644][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:55.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.646][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:55.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:55.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.653][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:55.654][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:55.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.657][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.658][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:55.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:55.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.663][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:55.664][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:55.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.666][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.668][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:55.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:55.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.673][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:55.674][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:55.676][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.677][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.679][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:55.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:55.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.684][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:55.685][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:55.686][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.688][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.689][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:55.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:55.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.694][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:55.696][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:55.697][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.698][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.699][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:55.701][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:55.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.702][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.704][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:55.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:55.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.708][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:55.709][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:55.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.711][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.712][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:55.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:55.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.716][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:55.718][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:55.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.719][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.721][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:55.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:55.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.725][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:55.726][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:55.727][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.728][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.729][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:55.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:55.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.734][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:55.735][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:55.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.748][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.750][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:55.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:55.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:55.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:55.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:55.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:55.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:55.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:55.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:55.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:55.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:55.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:55.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:55.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:55.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:55.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:55.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:55.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:55.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:55.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:55.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:55.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:55.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:55.802][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-02-10 19:45:55.804][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:55.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:55.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:55.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:55.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:55.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:55.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:55.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:55.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:55.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:55.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:55.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:55.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:55.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:55.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:55.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:55.830][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-02-10 19:45:55.831][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:45:55.833][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-02-10 19:45:55.834][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:45:55.835][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:45:55.836][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:45:55.837][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:45:55.838][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:45:55.840][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:45:55.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:55.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:55.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:55.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:55.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:55.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:55.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:55.858][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-02-10 19:45:55.862][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:55.863][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:55.865][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-02-10 19:45:56.236][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-02-10 19:45:56.594][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:56.597][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-02-10 19:45:56.601][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-02-10 19:45:56.605][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-02-10 19:45:56.607][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:45:56.609][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:56.610][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:56.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:56.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:56.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:56.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:56.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:56.625][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:56.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:45:56.629][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:56.644][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:56.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.646][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:56.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:56.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.653][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:56.655][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:56.656][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.657][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.659][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:56.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:56.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.663][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:56.665][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:56.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.667][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.669][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:56.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:56.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.673][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:56.674][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:56.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.676][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.677][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:56.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:56.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.681][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:56.682][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:56.683][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.684][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.685][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:56.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:56.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.691][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:56.692][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:56.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.694][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.695][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:56.696][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:56.697][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.698][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.699][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:56.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:56.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.704][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:56.704][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:56.705][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.706][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:56.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:56.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.712][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:56.713][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:56.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.714][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.716][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:56.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:56.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.721][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:56.722][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:56.723][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.724][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.725][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:56.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:56.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.730][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:56.731][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:56.732][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.733][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.735][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:56.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:56.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:56.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:56.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:56.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:56.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:56.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:56.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:56.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:56.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:56.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:56.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:56.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:56.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:56.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:56.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:56.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:56.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:56.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:56.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:56.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:56.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:56.790][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-02-10 19:45:56.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:56.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:56.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.797][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:56.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:56.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:56.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:56.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:56.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:56.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:56.808][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:56.809][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:56.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:56.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:56.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:56.820][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:56.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:56.822][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-02-10 19:45:56.823][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:45:56.825][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-02-10 19:45:56.826][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:45:56.827][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:45:56.828][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:45:56.829][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:45:56.830][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:45:56.832][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:45:56.835][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:56.836][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:56.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:56.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:56.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:56.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:56.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:56.849][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-02-10 19:45:56.852][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:56.853][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:56.854][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-02-10 19:45:57.248][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-02-10 19:45:57.604][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:45:57.607][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-02-10 19:45:57.611][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-02-10 19:45:57.614][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-02-10 19:45:57.616][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:45:57.617][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:57.619][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:57.621][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:57.622][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:57.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:57.629][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:57.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:57.631][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:57.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:45:57.634][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:57.635][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:57.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.636][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:57.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:57.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.642][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:57.644][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:57.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.646][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.648][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:57.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:57.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.652][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:57.653][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:57.654][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.655][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.656][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:57.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:57.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.661][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:57.662][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:57.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.664][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.665][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:57.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:57.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.669][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:57.670][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:57.671][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.672][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.673][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:57.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:57.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.678][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:57.680][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:57.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.682][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.684][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:57.685][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:57.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.697][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.699][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:57.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:57.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.704][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:57.705][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:57.706][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.707][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:57.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:57.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.712][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:57.714][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:57.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.716][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.718][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:57.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:57.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.722][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:57.724][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:57.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.726][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.728][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:57.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:57.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.734][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:57.735][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:57.736][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.738][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.739][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:57.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:57.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.745][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:57.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:57.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.750][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:57.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:57.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:57.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:57.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:57.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:57.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:57.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:57.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:57.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:57.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:57.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:57.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:57.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:57.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:57.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:57.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:57.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:57.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:57.791][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-02-10 19:45:57.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:57.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:57.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:57.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:57.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:57.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:57.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:57.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:57.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:57.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:57.808][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:57.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:57.815][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:57.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:57.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:57.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:57.820][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-02-10 19:45:57.821][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:45:57.823][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-02-10 19:45:57.824][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:45:57.826][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:45:57.827][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:45:57.828][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:45:57.829][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:45:57.830][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:45:57.834][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:57.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:57.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:57.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:57.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:57.845][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:57.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:45:57.848][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-02-10 19:45:57.859][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:57.860][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:57.862][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-02-10 19:45:58.250][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-02-10 19:45:58.602][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2025-02-10 19:45:58.604][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-02-10 19:45:58.606][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-02-10 19:45:58.610][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-02-10 19:45:58.614][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-02-10 19:45:58.616][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:45:58.617][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:45:58.618][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:45:58.620][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:45:58.622][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:45:58.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:45:58.630][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:45:58.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:45:58.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:45:58.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:45:58.635][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:58.637][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:58.637][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.638][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:58.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:58.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.645][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:58.646][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:58.647][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.649][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.650][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:45:58.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:45:58.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.655][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:58.656][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:58.657][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.658][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.659][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:45:58.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:45:58.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.664][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:58.665][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:58.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.667][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.668][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:45:58.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:45:58.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.673][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:58.674][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:58.674][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.675][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.677][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:45:58.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:45:58.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.681][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:58.682][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:45:58.684][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.685][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.686][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:58.688][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:58.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.690][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.692][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:45:58.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:58.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.697][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:58.698][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:58.699][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.700][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:58.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:45:58.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.707][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:58.708][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:58.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.711][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.713][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:45:58.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:45:58.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.717][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:58.718][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:58.719][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.720][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.721][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:45:58.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:45:58.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.725][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:58.727][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:58.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.729][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.730][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:45:58.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:45:58.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:58.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:58.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:58.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:58.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:58.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:58.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:45:58.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:45:58.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:58.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:58.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:58.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:58.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:58.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:58.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:58.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:58.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:58.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:58.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:45:58.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:45:58.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:58.797][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-02-10 19:45:58.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:58.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:58.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:58.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:58.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:45:58.806][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:58.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:45:58.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:45:58.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:45:58.853][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[2025-02-10 19:45:58.858][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:45:58.859][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:45:58.863][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-02-10 19:45:59.460][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-02-10 19:46:00.030][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:46:00.032][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-02-10 19:46:00.038][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-02-10 19:46:00.042][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:00.043][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:00.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:00.052][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:00.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:00.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:00.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:00.057][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.068][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:00.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:00.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:00.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:00.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:00.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:00.084][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:00.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:00.087][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.111][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:00.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:00.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:00.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:00.132][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:00.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:00.134][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:00.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:00.137][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.143][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.148][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:00.164][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:00.165][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:00.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:00.173][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:00.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:00.176][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:00.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:00.178][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.184][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:00.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:00.205][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:00.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:00.213][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:00.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:00.215][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:00.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:00.217][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.222][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:00.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:00.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:00.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:00.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:00.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:00.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:00.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:00.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.253][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:00.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:00.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:00.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:00.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:00.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:00.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:00.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:00.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:00.301][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:00.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:00.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:00.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:00.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:00.314][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:00.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:00.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.326][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:00.331][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:00.332][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:00.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:00.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:00.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:00.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:00.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:00.346][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:00.361][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:00.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:00.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:00.371][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:00.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:00.374][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:00.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:00.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.382][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:00.393][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:00.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:00.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:00.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:00.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:00.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:00.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:00.408][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.414][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.419][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:00.424][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:00.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:00.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:00.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:00.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:00.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:00.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:00.439][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.444][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:00.453][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:00.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:00.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:00.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:00.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:00.472][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:00.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:00.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.480][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.485][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:00.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:00.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:00.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:00.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:00.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:00.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:00.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:00.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.510][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:00.521][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:00.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:00.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:00.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:00.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:00.533][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:00.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:00.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.545][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:00.549][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:00.551][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:00.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:00.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:00.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:00.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:00.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:00.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:00.580][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:00.581][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:00.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:00.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:00.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:00.592][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:00.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:00.594][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.604][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:00.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:00.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:00.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:00.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:00.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:00.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:00.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:00.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:00.647][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:00.647][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:00.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:00.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:00.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:00.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:00.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:00.661][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:00.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:00.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:00.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:00.687][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:00.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:00.689][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:00.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:00.692][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.703][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:00.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:00.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:00.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:00.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:00.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:00.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:00.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.752][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:00.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:00.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:00.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:00.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:00.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:00.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:00.802][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:46:00.807][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:46:00.809][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:46:00.812][private$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[2025-02-10 19:46:01.163][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[2025-02-10 19:46:01.553][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:46:01.556][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-02-10 19:46:01.563][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-02-10 19:46:01.567][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[2025-02-10 19:46:01.571][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:46:01.572][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:46:01.574][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-02-10 19:46:01.927][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-02-10 19:46:02.280][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:46:02.283][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-02-10 19:46:02.288][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-02-10 19:46:02.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:02.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:02.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:02.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:02.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:02.304][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:02.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:02.306][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-02-10 19:46:02.307][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:46:02.309][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-02-10 19:46:02.311][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:46:02.312][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:46:02.313][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:46:02.315][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:46:02.316][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:46:02.317][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:46:02.320][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:02.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:02.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:02.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:02.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:02.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:02.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:02.335][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-02-10 19:46:02.339][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:46:02.340][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:46:02.341][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-02-10 19:46:02.723][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-02-10 19:46:03.096][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:46:03.099][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-02-10 19:46:03.103][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-02-10 19:46:03.107][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-02-10 19:46:03.109][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:46:03.111][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:46:03.113][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:46:03.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:03.117][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:03.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:03.125][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:03.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:03.128][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:03.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:03.132][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:03.133][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:03.134][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.136][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:03.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:03.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.141][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:46:03.143][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:46:03.144][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.145][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.146][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:46:03.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:46:03.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.151][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:46:03.152][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:46:03.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.154][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.156][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:46:03.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:46:03.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.161][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:46:03.162][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:46:03.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.164][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.166][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:46:03.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:46:03.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.170][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:46:03.171][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:46:03.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.189][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.191][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:46:03.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:46:03.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.196][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:46:03.197][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:46:03.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.199][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.200][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:46:03.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:46:03.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.204][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:46:03.205][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:03.206][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.208][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.209][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:46:03.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:03.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.213][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:03.214][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:03.215][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.216][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:03.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:03.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.223][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:46:03.224][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:46:03.225][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.226][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.227][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:46:03.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:46:03.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.232][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:46:03.233][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:46:03.235][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.236][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.238][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:46:03.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:46:03.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.243][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:46:03.244][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:46:03.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.246][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.248][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:46:03.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:46:03.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:03.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:03.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.259][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:03.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:03.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:03.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:03.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:03.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:03.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:03.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:03.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:03.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:03.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:03.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:03.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:03.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:03.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:03.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:03.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:03.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:03.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:03.302][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-02-10 19:46:03.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:03.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:03.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:03.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:03.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.312][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:03.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:03.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:03.316][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:03.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:03.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:03.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:03.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:03.327][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:03.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:03.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:03.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:03.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:03.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:03.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:03.350][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:03.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:03.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:03.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:03.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:03.357][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:03.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:03.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:03.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:03.368][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:03.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:03.371][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-02-10 19:46:03.372][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:46:03.374][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-02-10 19:46:03.376][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:46:03.377][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:46:03.379][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:46:03.380][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:46:03.382][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:46:03.383][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:46:03.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:03.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:03.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:03.397][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:03.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:03.400][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:03.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:03.402][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-02-10 19:46:03.406][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:46:03.407][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:46:03.409][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-02-10 19:46:03.790][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-02-10 19:46:04.147][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:46:04.150][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-02-10 19:46:04.154][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-02-10 19:46:04.157][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-02-10 19:46:04.160][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:46:04.161][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:46:04.163][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:46:04.165][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:04.166][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:04.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:04.174][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:04.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:04.176][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:04.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:04.180][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:04.181][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:04.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.183][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:04.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:04.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.189][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:46:04.190][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:46:04.191][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.192][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.194][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:46:04.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:46:04.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.198][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:46:04.199][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:46:04.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.201][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.202][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:46:04.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:46:04.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.207][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:46:04.208][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:46:04.209][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.210][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.211][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:46:04.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:46:04.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.216][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:46:04.217][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:46:04.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.219][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.220][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:46:04.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:46:04.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.224][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:46:04.225][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:46:04.226][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.227][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.228][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:46:04.229][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:04.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.231][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.233][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:46:04.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:04.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.249][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.252][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.253][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.255][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.257][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.261][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:46:04.262][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:46:04.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.265][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.267][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:46:04.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:46:04.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.272][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:46:04.273][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:46:04.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.276][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.277][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:46:04.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:46:04.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.281][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:46:04.282][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:46:04.283][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.283][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.285][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:46:04.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:46:04.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:04.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:04.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:04.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:04.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:04.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:04.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:04.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:04.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:04.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:04.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:04.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:04.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:04.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:04.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:04.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:04.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:04.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:04.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:04.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:04.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:04.331][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-02-10 19:46:04.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:04.371][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:46:04.376][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 19:46:04.377][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-10 19:46:04.378][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:46:04.380][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-02-10 19:46:04.383][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:04.384][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:04.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:04.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:04.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:04.394][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:04.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:04.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:04.417][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:04.418][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:04.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:04.425][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:04.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:04.427][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:04.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:04.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:04.453][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:04.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:04.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:04.462][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:04.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:04.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:04.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:04.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.493][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.498][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:04.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:04.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:04.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:04.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:04.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:04.519][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:04.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:04.521][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:04.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:04.545][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:04.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:04.553][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:04.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:04.555][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:04.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:04.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:04.578][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:04.580][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:04.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:04.588][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:04.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:04.591][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:04.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:04.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:04.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:04.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:04.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:04.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:04.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:04.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:04.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:04.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.628][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:04.633][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:04.634][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:04.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:04.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:04.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:04.645][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:04.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:04.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.658][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:04.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:04.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:04.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:04.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:04.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:04.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:04.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:04.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:04.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:04.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:04.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:04.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:04.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:04.702][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:04.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:04.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:04.718][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:04.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:04.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:04.727][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:04.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:04.729][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:04.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:04.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:04.756][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:04.757][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:04.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:04.765][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:04.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:04.767][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:04.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:04.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.778][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:04.783][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:04.784][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:04.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:04.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:04.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:04.795][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:04.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:04.797][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:04.813][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:04.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:04.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:04.822][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:04.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:04.824][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:04.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:04.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:04.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:04.841][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:04.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:04.849][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:04.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:04.850][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:04.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:04.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:04.864][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:04.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:04.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:04.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:04.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:04.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:04.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:04.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:04.889][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:04.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:04.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:04.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:04.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:04.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:04.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:04.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:04.938][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:04.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:04.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:04.947][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:04.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:04.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:04.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:04.952][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:04.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:04.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:04.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:04.974][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:04.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:04.977][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:04.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:04.979][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:04.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:04.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:04.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:04.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:04.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:04.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:05.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:05.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:05.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:05.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:05.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.009][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:05.044][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:46:05.048][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 19:46:05.049][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-10 19:46:05.051][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:46:05.052][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-02-10 19:46:05.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:05.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:05.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:05.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:05.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:05.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:05.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:05.070][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:05.092][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:05.093][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:05.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:05.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:05.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:05.103][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:05.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:05.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:05.131][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:05.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:05.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:05.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:05.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:05.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:05.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:05.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.182][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:05.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:05.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:05.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:05.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:05.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:05.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:05.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:05.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.212][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:05.227][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:05.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:05.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:05.236][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:05.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:05.238][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:05.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:05.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.246][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.251][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:05.263][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:05.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:05.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:05.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:05.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:05.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:05.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:05.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:05.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:05.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:05.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:05.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:05.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:05.304][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:05.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:05.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:05.320][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:05.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:05.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:05.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:05.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:05.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:05.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:05.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.342][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:05.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:05.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:05.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:05.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:05.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:05.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:05.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:05.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:05.374][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:05.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:05.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:05.399][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:05.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:05.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:05.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:05.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:05.421][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:05.422][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:05.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:05.428][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:05.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:05.431][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:05.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:05.434][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:05.455][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:05.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:05.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:05.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:05.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:05.465][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:05.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:05.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.473][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:05.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:05.484][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:05.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:05.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:05.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:05.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:05.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:05.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:05.511][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:05.513][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:05.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:05.522][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:05.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:05.524][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:05.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:05.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:05.543][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:05.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:05.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:05.552][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:05.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:05.555][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:05.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:05.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:05.570][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:05.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:05.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:05.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:05.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:05.580][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:05.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:05.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.591][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:05.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:05.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:05.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:05.612][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:05.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:05.614][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:05.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:05.617][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:05.631][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:05.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:05.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:05.641][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:05.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:05.643][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:05.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:05.645][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.655][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:05.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:05.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:05.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:05.687][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:05.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:05.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:05.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:05.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:05.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:05.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:05.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:05.719][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:05.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:05.721][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:05.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:05.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.733][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:05.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.759][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-02-10 19:46:05.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-02-10 19:46:05.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-10 19:46:05.776][biodb::testThat]
biodb.INFO [2025-02-10 19:46:05.778][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-02-10 19:46:05.779][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:46:05.781][biodb::testThat]
biodb.TRACE[2025-02-10 19:46:05.784][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-10 19:46:05.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-10 19:46:05.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:05.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:05.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.963][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:05.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:05.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:05.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:05.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:05.972][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:05.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:05.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:05.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:05.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:05.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:05.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:05.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:05.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:05.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:05.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:06.003][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:46:06.007][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:46:06.008][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:46:06.010][private$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[2025-02-10 19:46:06.364][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[2025-02-10 19:46:06.712][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:46:06.714][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-02-10 19:46:06.719][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-02-10 19:46:06.723][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:06.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:06.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:06.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:06.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:06.734][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:06.735][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[2025-02-10 19:46:06.736][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:06.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:06.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:06.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:06.740][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:06.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:06.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:06.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:06.745][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:06.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:06.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:06.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:06.768][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[2025-02-10 19:46:06.772][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:46:06.773][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:46:06.775][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-02-10 19:46:07.135][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-02-10 19:46:07.486][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:46:07.488][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-02-10 19:46:07.492][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-02-10 19:46:07.496][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:07.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:07.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:07.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:07.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:07.508][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:07.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:07.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:07.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:07.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:07.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:07.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.520][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:07.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:07.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:07.524][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:07.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:07.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:07.534][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:07.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:07.536][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:07.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:07.538][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:07.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:07.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:07.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:07.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:07.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:07.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:07.556][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-10 19:46:07.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:07.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:07.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:07.566][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:07.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:07.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:07.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:07.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.581][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:07.581][private$selectFields]
biodb.TRACE[2025-02-10 19:46:07.582][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 19:46:07.583][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 19:46:07.584][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:07.586][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.587][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.589][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.590][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.592][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.593][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.595][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.596][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:07.598][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:07.599][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.600][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.603][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.604][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 19:46:07.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.633][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-02-10 19:46:07.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:07.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:07.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:07.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:07.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:07.646][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:07.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:07.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.658][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:07.659][private$selectFields]
biodb.TRACE[2025-02-10 19:46:07.660][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 19:46:07.661][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 19:46:07.663][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:07.664][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.666][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.667][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.668][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.670][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.671][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.673][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.674][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:07.675][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:07.676][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.677][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.678][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.679][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.680][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 19:46:07.682][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.699][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-10 19:46:07.701][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:07.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:07.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:07.712][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:07.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:07.715][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:07.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:07.717][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.727][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:07.729][private$selectFields]
biodb.TRACE[2025-02-10 19:46:07.730][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 19:46:07.731][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 19:46:07.733][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:07.734][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.736][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.737][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.739][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.740][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.741][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.743][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.744][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:07.745][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:07.746][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.748][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.751][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.752][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 19:46:07.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.758][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.763][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:07.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.768][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-02-10 19:46:07.769][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-10 19:46:07.770][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-10 19:46:07.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:07.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:07.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:07.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:07.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:07.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:07.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:07.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:07.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:07.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:07.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:07.880][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:07.881][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:07.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:07.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:07.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:07.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:07.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:07.893][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:46:07.896][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:46:07.897][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:46:07.898][private$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[2025-02-10 19:46:08.244][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[2025-02-10 19:46:08.597][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:46:08.599][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-02-10 19:46:08.605][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-02-10 19:46:08.609][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[2025-02-10 19:46:08.613][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:46:08.614][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:46:08.617][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-02-10 19:46:08.967][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-02-10 19:46:09.329][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:46:09.331][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-02-10 19:46:09.335][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-02-10 19:46:09.339][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:09.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:09.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:09.348][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:09.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:09.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:09.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:09.352][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:09.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:09.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:09.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:09.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:09.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:09.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:09.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:09.367][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:09.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:09.374][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:09.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:09.376][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:09.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:09.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:09.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:09.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:09.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:09.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:09.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:09.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:09.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:09.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:09.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:09.402][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:09.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:09.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:09.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:09.407][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:09.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:09.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.411][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:09.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:09.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:09.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:09.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:09.444][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-10 19:46:09.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:09.475][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:09.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:09.484][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:09.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:09.486][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:09.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:09.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.497][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:09.498][private$selectFields]
biodb.TRACE[2025-02-10 19:46:09.499][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 19:46:09.501][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 19:46:09.502][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:09.503][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.504][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.505][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.506][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.507][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.508][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.509][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.510][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.512][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:09.513][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:09.514][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.515][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.516][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.517][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.518][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 19:46:09.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.528][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.533][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-02-10 19:46:09.534][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:09.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:09.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:09.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:09.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:09.546][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:09.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:09.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.608][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:09.609][private$selectFields]
biodb.TRACE[2025-02-10 19:46:09.610][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 19:46:09.611][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 19:46:09.612][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:09.613][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.614][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.615][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.616][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.617][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.618][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.619][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.620][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:09.633][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:09.634][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.635][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.637][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.638][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 19:46:09.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.649][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-10 19:46:09.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:09.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:09.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:09.658][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:09.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:09.660][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:09.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:09.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.670][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:09.671][private$selectFields]
biodb.TRACE[2025-02-10 19:46:09.672][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 19:46:09.673][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 19:46:09.674][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:09.676][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.676][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.677][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.678][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.679][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.681][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.683][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.684][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:09.686][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:09.687][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.688][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.690][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.691][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 19:46:09.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.707][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-02-10 19:46:09.707][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-10 19:46:09.708][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-10 19:46:09.718][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-02-10 19:46:09.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-02-10 19:46:09.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-10 19:46:09.727][biodb::testThat]
biodb.INFO [2025-02-10 19:46:09.728][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-02-10 19:46:09.729][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:46:09.730][biodb::testThat]
biodb.TRACE[2025-02-10 19:46:09.734][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-10 19:46:09.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-10 19:46:09.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.740][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.745][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.748][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.752][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:09.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:09.760][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:09.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:09.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:09.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:09.770][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:09.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:09.775][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:46:09.779][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 19:46:09.780][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-02-10 19:46:09.782][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:46:09.783][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-02-10 19:46:09.786][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:09.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:09.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:09.794][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:09.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:09.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:09.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:09.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.805][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:09.809][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:46:09.812][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 19:46:09.813][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-02-10 19:46:09.815][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:46:09.816][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-02-10 19:46:09.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:09.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:09.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:09.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:09.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:09.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:09.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:09.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:09.853][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:09.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:09.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:09.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:09.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:09.863][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:09.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:09.865][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.869][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.873][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:09.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:09.878][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-10 19:46:09.880][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:09.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:09.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:09.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:09.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:09.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:09.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:09.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.901][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:09.902][private$selectFields]
biodb.TRACE[2025-02-10 19:46:09.903][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 19:46:09.904][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 19:46:09.905][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:09.906][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.907][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.909][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.910][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.911][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.913][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.914][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:09.915][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:09.916][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.917][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.918][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.919][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.920][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 19:46:09.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.935][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-02-10 19:46:09.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:09.938][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:09.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:09.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:09.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:09.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:09.947][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.TRACE[2025-02-10 19:46:09.948][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.956][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:09.957][private$selectFields]
biodb.TRACE[2025-02-10 19:46:09.958][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 19:46:09.959][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 19:46:09.960][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:09.961][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.963][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.965][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.966][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.967][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.969][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.975][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:09.977][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:09.978][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.980][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.982][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.984][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 19:46:09.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:09.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:09.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:09.996][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-10 19:46:09.997][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:09.998][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:09.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:10.005][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:10.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:10.007][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:10.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:10.010][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.018][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.019][private$selectFields]
biodb.TRACE[2025-02-10 19:46:10.020][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 19:46:10.021][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 19:46:10.023][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.024][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.025][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.026][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.027][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.028][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.029][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.031][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.033][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.034][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.035][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.036][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.037][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.038][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.039][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 19:46:10.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.048][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.052][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-02-10 19:46:10.053][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-10 19:46:10.054][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-10 19:46:10.063][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:10.080][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:10.081][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:10.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:10.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:10.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:10.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:10.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:10.093][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:46:10.096][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 19:46:10.098][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-02-10 19:46:10.100][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:46:10.101][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-02-10 19:46:10.104][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:46:10.108][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 19:46:10.109][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-02-10 19:46:10.111][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:46:10.112][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-02-10 19:46:10.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:10.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:10.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:10.124][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:10.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:10.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:10.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:10.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.138][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:10.142][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:10.143][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:10.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:10.151][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:10.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:10.153][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:10.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:10.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.165][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:10.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:10.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:10.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:10.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:10.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:10.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:10.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:10.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.193][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:10.198][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-10 19:46:10.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:10.201][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:10.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:10.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:10.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:10.211][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:10.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:10.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.224][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.225][private$selectFields]
biodb.TRACE[2025-02-10 19:46:10.226][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 19:46:10.227][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 19:46:10.228][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.229][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.230][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.232][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.233][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.234][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.235][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.236][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.237][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.238][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.239][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.240][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.240][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.242][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.243][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 19:46:10.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.252][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.256][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-02-10 19:46:10.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:10.259][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:10.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:10.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:10.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:10.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:10.270][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.TRACE[2025-02-10 19:46:10.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.276][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.281][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.282][private$selectFields]
biodb.TRACE[2025-02-10 19:46:10.283][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 19:46:10.285][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 19:46:10.286][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.287][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.289][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.290][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.291][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.293][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.294][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.295][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.296][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.297][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.299][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.300][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.301][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.302][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.303][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.304][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 19:46:10.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.318][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-10 19:46:10.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:10.320][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:10.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:10.327][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:10.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:10.329][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:10.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:10.331][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.335][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.338][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.339][private$selectFields]
biodb.TRACE[2025-02-10 19:46:10.340][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 19:46:10.341][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 19:46:10.342][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.343][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.344][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.345][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.346][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.347][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.348][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.349][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.350][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.351][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.357][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.358][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.361][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.362][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 19:46:10.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.367][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.375][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-02-10 19:46:10.376][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-10 19:46:10.377][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-10 19:46:10.387][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-02-10 19:46:10.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-02-10 19:46:10.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-10 19:46:10.397][biodb::testThat]
biodb.INFO [2025-02-10 19:46:10.399][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-02-10 19:46:10.400][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:46:10.400][biodb::testThat]
biodb.TRACE[2025-02-10 19:46:10.403][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-10 19:46:10.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-10 19:46:10.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.408][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.412][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.416][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.420][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:10.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:10.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:10.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:10.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:10.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:10.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:10.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:10.444][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:46:10.447][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 19:46:10.448][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-02-10 19:46:10.450][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:46:10.452][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-02-10 19:46:10.454][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:10.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:10.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:10.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:10.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:10.465][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:10.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:10.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.473][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:10.483][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:46:10.487][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 19:46:10.489][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-02-10 19:46:10.490][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:46:10.491][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-02-10 19:46:10.494][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:10.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:10.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:10.503][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:10.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:10.505][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:10.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:10.508][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:10.521][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:10.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:10.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:10.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:10.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:10.533][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:10.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:10.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.544][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:10.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:10.549][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-10 19:46:10.551][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:10.552][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:10.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:10.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:10.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:10.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:10.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:10.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.576][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.577][private$selectFields]
biodb.TRACE[2025-02-10 19:46:10.578][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 19:46:10.579][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 19:46:10.580][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.581][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.583][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.584][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.585][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.586][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.587][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.589][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.590][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.592][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.593][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.594][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.595][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.596][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.597][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 19:46:10.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.612][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-02-10 19:46:10.613][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:10.614][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:10.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:10.623][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:10.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:10.625][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:10.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:10.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.636][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.637][private$selectFields]
biodb.TRACE[2025-02-10 19:46:10.638][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 19:46:10.639][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 19:46:10.640][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.641][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.643][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.644][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.645][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.646][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.647][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.649][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.650][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.651][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.652][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.653][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.654][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.655][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.656][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 19:46:10.657][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.667][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.672][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-10 19:46:10.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:10.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:10.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:10.682][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:10.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:10.685][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:10.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:10.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.697][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.698][private$selectFields]
biodb.TRACE[2025-02-10 19:46:10.698][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 19:46:10.699][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 19:46:10.700][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.701][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.703][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.704][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.705][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.706][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.707][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.709][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.709][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.711][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.712][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.713][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.714][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.716][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 19:46:10.717][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.721][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.726][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.732][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-02-10 19:46:10.733][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-10 19:46:10.734][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-10 19:46:10.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:10.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:10.789][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:10.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:10.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:10.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:10.798][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:10.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:10.802][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:46:10.806][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 19:46:10.807][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-02-10 19:46:10.809][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:46:10.811][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-02-10 19:46:10.813][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:46:10.816][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 19:46:10.818][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-02-10 19:46:10.819][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:46:10.820][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-02-10 19:46:10.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:10.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:10.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:10.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:10.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:10.834][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:10.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:10.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:10.848][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:10.849][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:10.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:10.857][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:10.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:10.859][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:10.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:10.861][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.865][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:10.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:10.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:10.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:10.882][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:10.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:10.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:10.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:10.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.896][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:10.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:10.901][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-10 19:46:10.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:10.903][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:10.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:10.911][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:10.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:10.913][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:10.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:10.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.924][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.925][private$selectFields]
biodb.TRACE[2025-02-10 19:46:10.926][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 19:46:10.927][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 19:46:10.928][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.929][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.930][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.932][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.933][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.934][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.935][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.936][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.938][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.939][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.940][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.941][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.943][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.944][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 19:46:10.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.948][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.956][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-02-10 19:46:10.957][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:10.958][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:10.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:10.965][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:10.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:10.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:10.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:10.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.974][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.978][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.979][private$selectFields]
biodb.TRACE[2025-02-10 19:46:10.980][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 19:46:10.981][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 19:46:10.982][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.983][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.984][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.985][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.986][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.987][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.988][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.989][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.990][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.991][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.993][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:10.994][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.995][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:10.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:10.997][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:10.998][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 19:46:10.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:11.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:11.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:11.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:11.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:11.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:11.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:11.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:11.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:11.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:11.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:11.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:11.011][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-10 19:46:11.013][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:11.014][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:11.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:11.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:11.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:11.024][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:11.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:11.026][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:11.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:11.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:11.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:11.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:11.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:11.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:11.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:11.035][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:11.036][private$selectFields]
biodb.TRACE[2025-02-10 19:46:11.037][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 19:46:11.038][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 19:46:11.039][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:11.040][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:11.041][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:11.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:11.043][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:11.044][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:11.045][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:11.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:11.046][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:11.047][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:11.048][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 19:46:11.049][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:11.050][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:11.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:11.052][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:11.054][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 19:46:11.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:11.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:11.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:11.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:11.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:11.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:11.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:11.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:11.063][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:11.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:11.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:11.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:11.067][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-02-10 19:46:11.068][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-10 19:46:11.069][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-10 19:46:11.098][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-02-10 19:46:11.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-02-10 19:46:11.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:11.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-10 19:46:11.110][biodb::testThat]
biodb.INFO [2025-02-10 19:46:11.111][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-02-10 19:46:11.112][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:46:11.113][biodb::testThat]
biodb.DEBUG[2025-02-10 19:46:11.115][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-02-10 19:46:11.117][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:46:11.118][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-02-10 19:46:11.120][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:46:11.121][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:46:11.123][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:46:11.124][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:46:11.125][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:46:11.127][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:46:11.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:11.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:11.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:11.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:11.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:11.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:11.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:11.145][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-02-10 19:46:11.149][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:46:11.150][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:46:11.151][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-02-10 19:46:11.623][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-02-10 19:46:11.986][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:46:11.996][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-02-10 19:46:12.007][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-02-10 19:46:12.011][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-02-10 19:46:12.014][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:46:12.015][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:46:12.017][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:46:12.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:12.020][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:12.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:12.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:12.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:12.029][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:12.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:12.033][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:12.035][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:12.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:12.037][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:12.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:12.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:12.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:12.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:12.043][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:46:12.044][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:46:12.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:12.046][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:12.047][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:46:12.048][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:46:12.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:12.050][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:12.051][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:46:12.052][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:46:12.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:12.054][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:12.056][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:46:12.057][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:46:12.058][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:12.059][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:12.061][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:46:12.062][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:46:12.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:12.065][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:12.066][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:46:12.068][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:12.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:12.070][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:12.072][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:12.073][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:12.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:12.075][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:12.076][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:46:12.077][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:46:12.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:12.079][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:12.081][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:46:12.082][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:46:12.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:12.083][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:12.084][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:46:12.085][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:46:12.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:12.088][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:12.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:12.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:12.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:12.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:12.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:12.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:12.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:12.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:12.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:12.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:12.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:12.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:12.103][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:12.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:12.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:12.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:12.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:12.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:12.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:12.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:12.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:12.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:12.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:12.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:12.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:12.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:12.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:12.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:12.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:12.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:12.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:12.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:12.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:12.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:12.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:12.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:12.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:12.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:12.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:12.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:12.136][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-02-10 19:46:12.137][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-02-10 19:46:12.148][biodb::testThat]
biodb.INFO [2025-02-10 19:46:12.149][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-02-10 19:46:12.150][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:46:12.151][biodb::testThat]
biodb.DEBUG[2025-02-10 19:46:12.162][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-02-10 19:46:12.164][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-02-10 19:46:12.165][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-02-10 19:46:12.168][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-02-10 19:46:12.170][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-02-10 19:46:12.171][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:46:12.172][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:46:12.173][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:46:12.174][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:46:12.175][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:46:12.180][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:12.182][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:12.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:12.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:12.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:12.193][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:12.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:12.196][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-02-10 19:46:12.199][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:46:12.200][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:46:12.202][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-02-10 19:46:12.557][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-02-10 19:46:12.902][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:46:12.905][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-02-10 19:46:12.909][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-02-10 19:46:12.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:12.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:12.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:12.921][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:12.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:12.923][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:12.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:12.925][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-02-10 19:46:12.929][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:46:12.930][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:46:12.932][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-02-10 19:46:13.279][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-02-10 19:46:13.641][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:46:13.644][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-02-10 19:46:13.648][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-02-10 19:46:13.651][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:13.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:13.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:13.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:13.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:13.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:13.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:13.664][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-02-10 19:46:13.667][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:46:13.668][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:46:13.670][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-02-10 19:46:14.046][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-02-10 19:46:14.406][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:46:14.409][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-02-10 19:46:14.413][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-02-10 19:46:14.417][private$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[2025-02-10 19:46:14.420][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:46:14.421][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-02-10 19:46:14.423][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-02-10 19:46:14.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:14.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:14.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:14.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:14.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:14.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:14.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:14.440][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.460][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.463][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.470][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:46:14.471][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:46:14.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.473][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.475][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:46:14.476][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:46:14.477][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.478][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.480][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:46:14.481][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:46:14.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.483][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.484][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:46:14.486][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:46:14.487][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.487][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.489][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:46:14.490][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:46:14.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.491][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.493][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:46:14.494][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:14.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.497][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.498][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:14.500][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:14.501][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.502][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.504][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:46:14.505][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:46:14.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.508][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.509][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:46:14.510][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:46:14.511][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.512][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.514][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:46:14.515][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:46:14.516][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.517][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:14.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:14.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:14.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:14.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:14.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:14.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:14.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:14.556][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:14.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:14.564][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:14.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:14.567][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:14.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:14.571][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.572][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.580][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.596][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.603][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:46:14.605][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:46:14.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.607][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.609][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:46:14.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:46:14.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.614][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:46:14.615][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:46:14.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.617][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.618][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:46:14.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:46:14.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.623][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:46:14.624][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:46:14.625][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.626][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.627][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:46:14.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:46:14.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.631][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:46:14.632][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:46:14.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.634][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.635][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:46:14.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:46:14.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.640][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:46:14.641][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:46:14.642][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.643][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.645][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:46:14.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:46:14.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.649][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:46:14.651][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:14.652][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.653][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.654][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:46:14.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:14.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.659][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:14.660][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:14.661][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.662][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:14.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:14.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.668][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:46:14.670][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:46:14.671][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.672][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.673][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:46:14.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:46:14.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.677][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:46:14.678][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:46:14.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.680][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.681][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:46:14.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:46:14.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.686][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:46:14.687][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:46:14.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.689][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.690][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:46:14.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:46:14.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:14.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:14.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:14.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:14.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.709][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:14.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:14.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:14.727][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:14.728][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:14.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:14.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:14.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:14.738][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:14.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:14.742][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.743][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.744][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.750][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:46:14.751][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:46:14.753][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.754][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.755][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:46:14.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:46:14.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.761][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:46:14.762][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:46:14.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.764][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.765][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:46:14.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:46:14.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.770][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:46:14.772][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:46:14.773][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.774][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.776][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:46:14.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:46:14.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.781][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:46:14.783][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:46:14.784][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.785][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.786][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:46:14.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:46:14.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.791][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:46:14.792][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:46:14.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.794][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.795][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:46:14.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:46:14.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.800][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:46:14.801][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:14.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.804][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.805][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:46:14.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:14.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.808][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:14.809][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:14.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.811][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:14.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:14.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.816][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:46:14.817][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:46:14.818][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.818][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.820][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:46:14.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:46:14.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.823][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:46:14.824][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:46:14.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.826][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.827][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:46:14.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:46:14.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.831][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:46:14.832][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:46:14.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.834][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.835][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:46:14.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:46:14.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.839][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:14.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:14.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:14.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:14.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.850][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:14.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:14.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:14.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:14.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:14.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:14.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:14.902][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-02-10 19:46:14.902][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-02-10 19:46:14.903][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-02-10 19:46:14.919][biodb::testThat]
biodb.INFO [2025-02-10 19:46:14.920][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-02-10 19:46:14.921][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:46:14.922][biodb::testThat]
biodb.INFO [2025-02-10 19:46:14.954][biodb::testThat]
biodb.INFO [2025-02-10 19:46:14.955][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-02-10 19:46:14.956][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:46:14.957][biodb::testThat]
biodb.INFO [2025-02-10 19:46:14.975][biodb::testThat]
biodb.INFO [2025-02-10 19:46:14.976][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-02-10 19:46:14.977][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:46:14.978][biodb::testThat]
biodb.DEBUG[2025-02-10 19:46:14.981][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:46:15.001][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:46:15.003][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:46:15.004][private$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[2025-02-10 19:46:15.515][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[2025-02-10 19:46:16.049][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:46:16.052][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-02-10 19:46:16.057][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-02-10 19:46:16.075][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:46:16.076][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:46:16.077][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:16.078][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:16.079][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:16.080][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:16.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:16.082][ef$get] fields variable is a list.
biodb.INFO [2025-02-10 19:46:16.083][biodb::testThat]
biodb.INFO [2025-02-10 19:46:16.084][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2025-02-10 19:46:16.085][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:46:16.086][biodb::testThat]
biodb.ERROR[2025-02-10 19:46:16.104][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-02-10 19:46:16.123][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-02-10 19:46:16.140][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-10 19:46:16.142][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-02-10 19:46:16.143][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-02-10 19:46:16.144][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-10 19:46:16.145][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:16.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:16.147][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.149][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-02-10 19:46:16.164][biodb::testContext]
biodb.INFO [2025-02-10 19:46:16.165][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-10 19:46:16.166][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-02-10 19:46:16.167][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-10 19:46:16.167][biodb::testContext]
biodb.INFO [2025-02-10 19:46:16.169][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-10 19:46:16.171][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-02-10 19:46:16.175][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 19:46:16.176][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-10 19:46:16.177][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-10 19:46:16.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.180][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-10 19:46:16.181][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-10 19:46:16.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.184][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-10 19:46:16.185][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-10 19:46:16.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.188][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-10 19:46:16.189][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-10 19:46:16.190][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-10 19:46:16.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.193][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[2025-02-10 19:46:16.194][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-10 19:46:16.195][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-10 19:46:16.196][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-10 19:46:16.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.200][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-10 19:46:16.201][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-10 19:46:16.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.205][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-10 19:46:16.206][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-10 19:46:16.208][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-10 19:46:16.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.211][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-10 19:46:16.213][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-10 19:46:16.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.217][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-10 19:46:16.218][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-10 19:46:16.219][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-10 19:46:16.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.224][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-10 19:46:16.225][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-10 19:46:16.226][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-10 19:46:16.227][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-10 19:46:16.229][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-10 19:46:16.230][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-10 19:46:16.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.233][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[2025-02-10 19:46:16.234][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-10 19:46:16.236][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-10 19:46:16.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.239][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-10 19:46:16.240][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-10 19:46:16.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.243][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[2025-02-10 19:46:16.244][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-10 19:46:16.245][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-10 19:46:16.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.249][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-10 19:46:16.250][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-10 19:46:16.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.254][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-10 19:46:16.256][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-10 19:46:16.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.261][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-10 19:46:16.262][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-10 19:46:16.294][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-10 19:46:16.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.298][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-10 19:46:16.299][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-10 19:46:16.301][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-10 19:46:16.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.304][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-10 19:46:16.306][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:16.307][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-10 19:46:16.309][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:16.310][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 19:46:16.311][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:16.313][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 19:46:16.314][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:16.315][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 19:46:16.316][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-10 19:46:16.317][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 19:46:16.318][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:16.319][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-10 19:46:16.320][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 19:46:16.321][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:16.322][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:16.323][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 19:46:16.323][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 19:46:16.323][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 19:46:16.323][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-10 19:46:16.323][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-10 19:46:16.324][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 19:46:16.325][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:16.326][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:16.328][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 19:46:16.329][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:16.330][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:16.331][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 19:46:16.332][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:16.333][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 19:46:16.334][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 19:46:16.335][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:16.336][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:16.338][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-10 19:46:16.340][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:16.341][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-10 19:46:16.342][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:16.344][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 19:46:16.345][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:16.347][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 19:46:16.348][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:16.349][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 19:46:16.350][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-10 19:46:16.352][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 19:46:16.353][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:16.354][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-10 19:46:16.356][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 19:46:16.357][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:16.358][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:16.359][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 19:46:16.359][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 19:46:16.359][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 19:46:16.359][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-10 19:46:16.359][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-10 19:46:16.361][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 19:46:16.362][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:16.364][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:16.365][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 19:46:16.366][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:16.367][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:16.368][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 19:46:16.370][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:16.371][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 19:46:16.372][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 19:46:16.374][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:16.375][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:16.377][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-10 19:46:16.379][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:16.381][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-10 19:46:16.382][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:16.383][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 19:46:16.385][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:16.386][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 19:46:16.387][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:16.389][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 19:46:16.390][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-10 19:46:16.391][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 19:46:16.393][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:16.394][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-10 19:46:16.396][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 19:46:16.397][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:16.398][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:16.400][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:16.401][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 19:46:16.403][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:16.404][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:16.405][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 19:46:16.407][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:16.408][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:16.409][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 19:46:16.410][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:16.412][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 19:46:16.413][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 19:46:16.414][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:16.416][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:16.417][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-10 19:46:16.420][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:16.435][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-10 19:46:16.437][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:16.438][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 19:46:16.439][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:16.441][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 19:46:16.442][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:16.444][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 19:46:16.445][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-10 19:46:16.446][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 19:46:16.447][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:16.448][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-10 19:46:16.450][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 19:46:16.451][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:16.452][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:16.454][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:16.455][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 19:46:16.456][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:16.457][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:16.458][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 19:46:16.459][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:16.461][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:16.462][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 19:46:16.463][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:16.464][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 19:46:16.465][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 19:46:16.466][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:16.467][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:16.469][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 19:46:16.470][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.471][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[2025-02-10 19:46:16.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.477][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[2025-02-10 19:46:16.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.502][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[2025-02-10 19:46:16.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.517][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[2025-02-10 19:46:16.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.527][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[2025-02-10 19:46:16.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.557][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-10 19:46:16.558][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-10 19:46:16.560][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-10 19:46:16.561][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-10 19:46:16.562][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-10 19:46:16.563][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-10 19:46:16.565][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-10 19:46:16.566][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-10 19:46:16.567][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-10 19:46:16.568][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-10 19:46:16.570][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-10 19:46:16.571][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-10 19:46:16.572][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-10 19:46:16.574][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-10 19:46:16.575][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-10 19:46:16.576][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-10 19:46:16.577][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-10 19:46:16.579][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-10 19:46:16.580][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-10 19:46:16.582][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-10 19:46:16.584][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-10 19:46:16.586][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-10 19:46:16.587][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-10 19:46:16.588][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-10 19:46:16.590][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-10 19:46:16.591][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-10 19:46:16.593][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-10 19:46:16.594][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-10 19:46:16.596][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-10 19:46:16.598][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-10 19:46:16.599][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-10 19:46:16.601][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-10 19:46:16.603][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-10 19:46:16.604][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-10 19:46:16.606][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-10 19:46:16.607][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-10 19:46:16.608][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-10 19:46:16.610][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-10 19:46:16.612][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-10 19:46:16.613][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-10 19:46:16.614][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-10 19:46:16.615][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-10 19:46:16.617][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-10 19:46:16.619][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-10 19:46:16.621][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-10 19:46:16.624][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-10 19:46:16.626][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-10 19:46:16.628][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-10 19:46:16.631][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-10 19:46:16.633][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-10 19:46:16.635][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-10 19:46:16.637][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-10 19:46:16.638][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-10 19:46:16.640][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-10 19:46:16.641][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-10 19:46:16.643][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-10 19:46:16.645][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-10 19:46:16.646][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-10 19:46:16.647][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-10 19:46:16.649][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-10 19:46:16.651][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-10 19:46:16.653][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-10 19:46:16.654][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-10 19:46:16.656][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-10 19:46:16.657][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-10 19:46:16.659][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-10 19:46:16.660][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-10 19:46:16.661][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-10 19:46:16.663][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-10 19:46:16.665][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-10 19:46:16.667][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-10 19:46:16.669][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-10 19:46:16.671][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-10 19:46:16.673][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-10 19:46:16.675][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-10 19:46:16.677][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-10 19:46:16.678][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-10 19:46:16.680][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-10 19:46:16.682][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-10 19:46:16.684][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-10 19:46:16.686][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-10 19:46:16.688][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-10 19:46:16.689][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-10 19:46:16.690][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-10 19:46:16.693][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-10 19:46:16.694][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 19:46:16.695][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.697][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:16.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:16.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:16.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:16.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:16.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:16.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:16.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:16.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.730][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[2025-02-10 19:46:16.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:16.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:16.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:16.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:16.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:16.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:16.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:16.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:16.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:16.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:16.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:16.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:16.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:16.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:16.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:16.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:16.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:16.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:16.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:16.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:16.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:16.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:16.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.813][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[2025-02-10 19:46:16.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:16.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:16.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:16.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:16.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:16.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:16.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:16.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:16.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:16.827][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-02-10 19:46:16.829][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-02-10 19:46:16.832][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:16.833][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-10 19:46:16.834][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:16.836][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 19:46:16.837][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:16.838][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 19:46:16.839][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:16.840][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-02-10 19:46:16.841][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-10 19:46:16.842][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 19:46:16.843][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:16.844][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-02-10 19:46:16.845][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 19:46:16.846][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-02-10 19:46:16.846][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-02-10 19:46:16.846][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-02-10 19:46:16.846][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-02-10 19:46:16.846][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-02-10 19:46:16.846][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-02-10 19:46:16.846][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-02-10 19:46:16.846][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-02-10 19:46:16.846][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-02-10 19:46:16.846][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-02-10 19:46:16.846][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-02-10 19:46:16.847][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:16.848][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 19:46:16.848][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 19:46:16.848][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 19:46:16.849][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-10 19:46:16.850][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:16.851][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:16.852][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 19:46:16.853][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:16.854][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:16.855][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 19:46:16.857][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:46:16.857][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-02-10 19:46:16.858][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 19:46:16.859][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 19:46:16.860][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:16.861][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-02-10 19:46:16.861][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-02-10 19:46:16.862][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-10 19:46:16.864][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-10 19:46:16.865][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-02-10 19:46:16.866][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-10 19:46:16.868][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-10 19:46:16.869][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-10 19:46:16.872][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-02-10 19:46:16.873][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-02-10 19:46:16.874][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-02-10 19:46:16.875][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-02-10 19:46:16.877][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-10 19:46:16.878][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-10 19:46:16.879][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-02-10 19:46:16.880][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-02-10 19:46:16.881][biodb::testThat]
biodb.INFO [2025-02-10 19:46:16.882][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2025-02-10 19:46:16.884][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:46:16.884][biodb::testThat]
biodb.DEBUG[2025-02-10 19:46:16.889][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-02-10 19:46:16.893][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:46:16.894][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:46:16.895][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-02-10 19:46:17.232][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-02-10 19:46:17.735][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:46:17.737][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-02-10 19:46:17.741][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-02-10 19:46:17.745][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:46:17.749][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:46:17.750][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:46:17.752][private$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[2025-02-10 19:46:18.102][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[2025-02-10 19:46:18.454][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:46:18.457][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-02-10 19:46:18.462][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-02-10 19:46:18.465][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:18.466][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:18.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:18.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:18.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:18.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:18.477][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[2025-02-10 19:46:18.478][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[2025-02-10 19:46:18.482][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:46:18.483][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:46:18.485][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-02-10 19:46:18.845][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-02-10 19:46:19.194][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:46:19.197][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-02-10 19:46:19.201][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-02-10 19:46:19.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:19.205][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:19.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:19.214][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:19.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:19.216][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:19.217][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[2025-02-10 19:46:19.234][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:19.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:19.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:19.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:19.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:19.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:19.245][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.DEBUG[2025-02-10 19:46:19.250][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:46:19.254][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 19:46:19.255][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-02-10 19:46:19.256][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:46:19.258][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-02-10 19:46:19.260][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:19.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:19.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:19.269][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:19.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:19.271][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:19.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:19.275][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:46:19.278][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 19:46:19.279][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-02-10 19:46:19.280][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:46:19.282][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-02-10 19:46:19.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:19.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:19.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:19.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:19.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:19.294][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:19.294][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[2025-02-10 19:46:19.295][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:19.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:19.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:19.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:19.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:19.306][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:19.308][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[2025-02-10 19:46:19.312][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:46:19.316][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 19:46:19.318][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-02-10 19:46:19.319][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:46:19.321][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-02-10 19:46:19.323][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:19.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:19.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:19.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:19.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:19.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:19.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:19.336][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:46:19.340][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 19:46:19.342][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-02-10 19:46:19.343][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:46:19.344][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-02-10 19:46:19.346][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:19.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:19.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:19.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:19.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:19.358][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:19.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:19.360][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:46:19.364][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:46:19.365][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:46:19.367][private$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[2025-02-10 19:46:19.719][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[2025-02-10 19:46:20.076][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:46:20.079][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-02-10 19:46:20.085][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-02-10 19:46:20.088][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:20.089][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:20.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:20.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:20.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:20.100][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:20.100][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.INFO [2025-02-10 19:46:20.111][biodb::testThat]
biodb.INFO [2025-02-10 19:46:20.112][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2025-02-10 19:46:20.113][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:46:20.114][biodb::testThat]
biodb.DEBUG[2025-02-10 19:46:20.117][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[2025-02-10 19:46:20.120][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:46:20.121][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:46:20.123][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-02-10 19:46:20.472][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-02-10 19:46:20.822][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:46:20.825][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-02-10 19:46:20.830][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-02-10 19:46:20.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:20.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:20.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:20.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:20.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:20.872][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:20.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:20.879][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:46:20.883][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:46:20.885][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:46:20.887][private$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[2025-02-10 19:46:21.250][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[2025-02-10 19:46:21.619][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:46:21.622][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-02-10 19:46:21.626][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-02-10 19:46:21.628][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:21.629][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:21.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:21.636][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:21.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:21.637][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-02-10 19:46:21.644][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-10 19:46:21.646][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-02-10 19:46:21.647][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-02-10 19:46:21.649][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-10 19:46:21.650][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:21.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:21.651][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:21.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:21.653][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-02-10 19:46:21.659][biodb::testContext]
biodb.INFO [2025-02-10 19:46:21.660][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-10 19:46:21.661][biodb::testContext] Test context - Test web services
biodb.INFO [2025-02-10 19:46:21.662][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-10 19:46:21.664][biodb::testContext]
biodb.INFO [2025-02-10 19:46:21.666][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-10 19:46:21.668][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-02-10 19:46:21.672][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 19:46:21.674][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-10 19:46:21.675][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-10 19:46:21.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.679][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-10 19:46:21.680][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-10 19:46:21.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.684][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-10 19:46:21.685][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-10 19:46:21.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.689][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-10 19:46:21.690][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-10 19:46:21.690][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-10 19:46:21.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.694][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-10 19:46:21.695][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-10 19:46:21.695][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-10 19:46:21.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.699][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-10 19:46:21.701][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-10 19:46:21.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.705][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-10 19:46:21.706][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-10 19:46:21.707][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-10 19:46:21.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.711][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-10 19:46:21.713][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-10 19:46:21.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.716][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-10 19:46:21.717][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-10 19:46:21.718][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-10 19:46:21.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.722][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-10 19:46:21.723][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-10 19:46:21.724][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-10 19:46:21.725][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-10 19:46:21.726][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-10 19:46:21.727][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-10 19:46:21.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.730][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[2025-02-10 19:46:21.731][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-10 19:46:21.732][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-10 19:46:21.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.736][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-10 19:46:21.738][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-10 19:46:21.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.741][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-10 19:46:21.743][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-10 19:46:21.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.747][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-10 19:46:21.748][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-10 19:46:21.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.751][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-10 19:46:21.753][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-10 19:46:21.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.757][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-10 19:46:21.758][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-10 19:46:21.782][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-10 19:46:21.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.786][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-10 19:46:21.788][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-10 19:46:21.789][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-10 19:46:21.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.793][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-10 19:46:21.794][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:21.795][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-10 19:46:21.796][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:21.797][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 19:46:21.798][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:21.799][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 19:46:21.800][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:21.801][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 19:46:21.803][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-10 19:46:21.804][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 19:46:21.805][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:21.806][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-10 19:46:21.807][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 19:46:21.808][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:21.810][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:21.811][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 19:46:21.811][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 19:46:21.811][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 19:46:21.811][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-10 19:46:21.811][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-10 19:46:21.812][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 19:46:21.813][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:21.814][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:21.815][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 19:46:21.817][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:21.818][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:21.819][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 19:46:21.820][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:21.821][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 19:46:21.822][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 19:46:21.823][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:21.824][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:21.826][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-10 19:46:21.828][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:21.830][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-10 19:46:21.831][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:21.832][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 19:46:21.834][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:21.834][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 19:46:21.835][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:21.836][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 19:46:21.837][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-10 19:46:21.838][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 19:46:21.839][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:21.840][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-10 19:46:21.841][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 19:46:21.842][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:21.843][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:21.844][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 19:46:21.844][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 19:46:21.844][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 19:46:21.844][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-10 19:46:21.844][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-10 19:46:21.845][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 19:46:21.846][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:21.847][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:21.848][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 19:46:21.850][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:21.851][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:21.852][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 19:46:21.853][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:21.854][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 19:46:21.855][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 19:46:21.857][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:21.858][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:21.859][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-10 19:46:21.861][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:21.862][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-10 19:46:21.863][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:21.864][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 19:46:21.865][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:21.867][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 19:46:21.867][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:21.869][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 19:46:21.870][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-10 19:46:21.871][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 19:46:21.872][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:21.873][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-10 19:46:21.874][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 19:46:21.875][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:21.877][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:21.878][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:21.879][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 19:46:21.880][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:21.881][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:21.882][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 19:46:21.883][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:21.884][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:21.885][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 19:46:21.886][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:21.888][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 19:46:21.888][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 19:46:21.889][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:21.891][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:21.892][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-10 19:46:21.894][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:21.895][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-10 19:46:21.897][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:21.897][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 19:46:21.899][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:21.899][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 19:46:21.900][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:21.901][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 19:46:21.903][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-10 19:46:21.904][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 19:46:21.905][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:21.906][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-10 19:46:21.907][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 19:46:21.908][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:21.909][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:21.910][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:21.911][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 19:46:21.913][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:21.914][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:21.915][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 19:46:21.916][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:21.917][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:21.918][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 19:46:21.919][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:21.921][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 19:46:21.923][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 19:46:21.924][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:21.925][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:21.927][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 19:46:21.928][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:21.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:21.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.934][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.DEBUG[2025-02-10 19:46:21.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:21.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:21.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.939][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[2025-02-10 19:46:21.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:21.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:21.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.943][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[2025-02-10 19:46:21.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:21.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:21.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:21.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:21.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.953][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.DEBUG[2025-02-10 19:46:21.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:21.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:21.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:21.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:21.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:21.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:21.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:21.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:21.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:21.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:21.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:21.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:21.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:21.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:21.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:21.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:21.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:21.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:22.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:22.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:22.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:22.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.012][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.DEBUG[2025-02-10 19:46:22.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:22.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.017][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[2025-02-10 19:46:22.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:22.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.022][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.DEBUG[2025-02-10 19:46:22.023][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-10 19:46:22.024][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-10 19:46:22.026][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-10 19:46:22.027][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-10 19:46:22.029][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-10 19:46:22.030][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-10 19:46:22.031][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-10 19:46:22.033][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-10 19:46:22.034][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-10 19:46:22.036][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-10 19:46:22.038][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-10 19:46:22.039][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-10 19:46:22.041][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-10 19:46:22.042][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-10 19:46:22.044][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-10 19:46:22.045][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-10 19:46:22.046][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-10 19:46:22.047][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-10 19:46:22.048][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-10 19:46:22.050][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-10 19:46:22.051][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-10 19:46:22.052][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-10 19:46:22.054][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-10 19:46:22.055][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-10 19:46:22.057][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-10 19:46:22.058][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-10 19:46:22.060][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-10 19:46:22.061][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-10 19:46:22.063][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-10 19:46:22.064][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-10 19:46:22.066][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-10 19:46:22.068][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-10 19:46:22.069][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-10 19:46:22.070][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-10 19:46:22.072][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-10 19:46:22.074][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-10 19:46:22.075][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-10 19:46:22.077][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-10 19:46:22.079][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-10 19:46:22.080][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-10 19:46:22.082][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-10 19:46:22.084][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-10 19:46:22.086][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-10 19:46:22.087][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-10 19:46:22.089][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-10 19:46:22.091][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-10 19:46:22.093][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-10 19:46:22.094][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-10 19:46:22.096][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-10 19:46:22.098][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-10 19:46:22.099][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-10 19:46:22.100][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-10 19:46:22.102][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-10 19:46:22.103][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-10 19:46:22.105][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-10 19:46:22.106][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-10 19:46:22.108][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-10 19:46:22.109][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-10 19:46:22.110][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-10 19:46:22.112][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-10 19:46:22.114][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-10 19:46:22.116][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-10 19:46:22.118][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-10 19:46:22.119][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-10 19:46:22.121][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-10 19:46:22.123][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-10 19:46:22.124][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-10 19:46:22.126][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-10 19:46:22.127][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-10 19:46:22.129][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-10 19:46:22.130][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-10 19:46:22.131][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-10 19:46:22.133][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-10 19:46:22.134][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-10 19:46:22.136][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-10 19:46:22.138][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-10 19:46:22.140][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-10 19:46:22.141][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-10 19:46:22.142][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-10 19:46:22.143][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-10 19:46:22.145][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-10 19:46:22.146][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-10 19:46:22.148][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-10 19:46:22.149][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-10 19:46:22.151][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-10 19:46:22.152][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 19:46:22.153][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.155][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:22.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:22.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:22.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:22.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:22.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:22.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:22.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:22.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.170][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[2025-02-10 19:46:22.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:22.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:22.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:22.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.176][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[2025-02-10 19:46:22.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:22.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:22.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:22.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:22.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:22.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:22.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:22.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:22.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:22.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:22.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:22.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.197][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[2025-02-10 19:46:22.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:22.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:22.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:22.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.205][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[2025-02-10 19:46:22.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:22.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:22.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:22.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.212][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[2025-02-10 19:46:22.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:22.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:22.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:22.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.218][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[2025-02-10 19:46:22.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:22.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:22.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:22.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:22.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:22.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:22.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:22.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:22.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:22.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:22.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:22.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:22.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:22.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:22.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:22.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:22.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:22.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:22.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:22.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:22.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:22.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:22.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:22.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.260][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[2025-02-10 19:46:22.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:22.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:22.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:22.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:22.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:22.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:22.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:22.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:22.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:22.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:22.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:22.275][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-02-10 19:46:22.277][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-02-10 19:46:22.280][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:22.281][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-10 19:46:22.282][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:22.283][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 19:46:22.285][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:22.286][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 19:46:22.287][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:22.288][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-02-10 19:46:22.290][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-10 19:46:22.291][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 19:46:22.292][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:22.293][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-02-10 19:46:22.293][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 19:46:22.294][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-02-10 19:46:22.294][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-02-10 19:46:22.294][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-02-10 19:46:22.294][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-02-10 19:46:22.294][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-02-10 19:46:22.294][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-02-10 19:46:22.294][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-02-10 19:46:22.294][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-02-10 19:46:22.294][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-02-10 19:46:22.294][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-02-10 19:46:22.294][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-02-10 19:46:22.296][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:22.297][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 19:46:22.297][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 19:46:22.297][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 19:46:22.298][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-10 19:46:22.299][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:22.300][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:22.301][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 19:46:22.302][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:22.304][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:22.305][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 19:46:22.306][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:46:22.306][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-02-10 19:46:22.308][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 19:46:22.309][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 19:46:22.310][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:22.312][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-02-10 19:46:22.312][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-02-10 19:46:22.313][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-10 19:46:22.315][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-10 19:46:22.317][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-02-10 19:46:22.319][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-10 19:46:22.321][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-10 19:46:22.323][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-10 19:46:22.327][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-02-10 19:46:22.328][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-02-10 19:46:22.330][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-02-10 19:46:22.332][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-02-10 19:46:22.334][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-10 19:46:22.335][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-10 19:46:22.337][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-02-10 19:46:22.338][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-02-10 19:46:22.340][biodb::testThat]
biodb.INFO [2025-02-10 19:46:22.341][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-02-10 19:46:22.342][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:46:22.344][biodb::testThat]
biodb.DEBUG[2025-02-10 19:46:22.356][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-02-10 19:46:22.361][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 19:46:22.362][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-02-10 19:46:22.364][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:46:22.366][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-02-10 19:46:22.371][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[2025-02-10 19:46:22.376][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:46:22.377][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:46:22.379][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-02-10 19:46:22.730][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-02-10 19:46:23.087][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:46:23.090][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-02-10 19:46:23.095][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-02-10 19:46:23.106][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-10 19:46:23.108][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-02-10 19:46:23.109][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-02-10 19:46:23.110][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-10 19:46:23.111][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:23.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:23.113][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:23.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:23.116][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-02-10 19:46:23.122][biodb::testContext]
biodb.INFO [2025-02-10 19:46:23.123][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-10 19:46:23.125][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-02-10 19:46:23.126][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-10 19:46:23.127][biodb::testContext]
biodb.INFO [2025-02-10 19:46:23.129][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-10 19:46:23.131][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-02-10 19:46:23.136][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 19:46:23.137][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-10 19:46:23.138][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-10 19:46:23.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.143][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-10 19:46:23.145][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-10 19:46:23.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.149][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-10 19:46:23.150][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-10 19:46:23.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.155][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-10 19:46:23.156][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-10 19:46:23.157][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-10 19:46:23.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.161][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-10 19:46:23.163][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-10 19:46:23.164][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-10 19:46:23.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.169][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-10 19:46:23.170][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-10 19:46:23.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.175][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-10 19:46:23.176][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-10 19:46:23.177][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-10 19:46:23.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.180][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-10 19:46:23.182][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-10 19:46:23.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.185][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-10 19:46:23.186][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-10 19:46:23.188][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-10 19:46:23.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.192][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-10 19:46:23.193][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-10 19:46:23.195][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-10 19:46:23.196][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-10 19:46:23.197][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-10 19:46:23.199][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-10 19:46:23.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.203][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-10 19:46:23.204][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-10 19:46:23.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.209][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-10 19:46:23.210][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-10 19:46:23.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.215][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-10 19:46:23.216][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-10 19:46:23.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.221][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-10 19:46:23.222][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-10 19:46:23.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.226][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-10 19:46:23.228][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-10 19:46:23.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.232][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-10 19:46:23.233][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-10 19:46:23.650][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-10 19:46:23.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.655][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-10 19:46:23.657][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-10 19:46:23.658][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-10 19:46:23.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.663][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-10 19:46:23.665][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:23.666][self$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[2025-02-10 19:46:23.667][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:23.668][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 19:46:23.669][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:23.670][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 19:46:23.672][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:23.673][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 19:46:23.674][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-10 19:46:23.675][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 19:46:23.677][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:23.678][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-10 19:46:23.679][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 19:46:23.681][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:23.682][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:23.683][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 19:46:23.683][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 19:46:23.683][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 19:46:23.683][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-10 19:46:23.683][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-10 19:46:23.685][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 19:46:23.686][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:23.687][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:23.688][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 19:46:23.689][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:23.691][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:23.692][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 19:46:23.693][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:23.695][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 19:46:23.696][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 19:46:23.697][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:23.698][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:23.700][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-10 19:46:23.702][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:23.704][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-10 19:46:23.705][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:23.706][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 19:46:23.707][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:23.709][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 19:46:23.710][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:23.712][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 19:46:23.713][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-10 19:46:23.714][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 19:46:23.715][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:23.717][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-10 19:46:23.718][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 19:46:23.719][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:23.721][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:23.722][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 19:46:23.722][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 19:46:23.722][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 19:46:23.722][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-10 19:46:23.722][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-10 19:46:23.723][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 19:46:23.724][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:23.725][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:23.726][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 19:46:23.727][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:23.728][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:23.729][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 19:46:23.730][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:23.731][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 19:46:23.732][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 19:46:23.734][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:23.735][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:23.736][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-10 19:46:23.738][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:23.739][self$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[2025-02-10 19:46:23.740][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:23.741][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 19:46:23.742][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:23.744][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 19:46:23.745][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:23.746][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 19:46:23.747][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-10 19:46:23.748][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 19:46:23.749][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:23.750][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-10 19:46:23.752][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 19:46:23.753][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:23.754][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:23.755][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:23.757][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 19:46:23.758][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:23.759][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:23.760][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 19:46:23.761][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:23.762][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:23.764][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 19:46:23.765][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:23.767][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 19:46:23.768][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 19:46:23.769][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:23.770][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:23.772][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-10 19:46:23.774][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:23.775][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-10 19:46:23.777][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:23.778][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 19:46:23.779][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:23.780][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 19:46:23.781][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:23.783][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 19:46:23.784][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-10 19:46:23.785][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 19:46:23.786][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:23.787][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-10 19:46:23.788][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 19:46:23.789][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:23.790][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:23.791][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:23.792][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 19:46:23.793][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:23.793][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:23.794][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 19:46:23.795][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:23.796][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:23.797][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 19:46:23.798][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:23.799][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 19:46:23.800][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 19:46:23.801][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:23.803][self$setPropertyValue]
biodb.DEBUG[2025-02-10 19:46:23.804][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 19:46:23.806][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:23.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:23.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:23.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:23.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.818][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[2025-02-10 19:46:23.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:23.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:23.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:23.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:23.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:23.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:23.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:23.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:23.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:23.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:23.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:23.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:23.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:23.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:23.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.857][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[2025-02-10 19:46:23.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:23.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:23.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:23.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:23.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.867][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.DEBUG[2025-02-10 19:46:23.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:23.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:23.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.881][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[2025-02-10 19:46:23.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:23.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:23.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:23.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:23.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:23.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:23.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:23.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:23.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:23.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:23.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:23.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:23.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:23.932][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-10 19:46:23.934][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-10 19:46:23.936][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-10 19:46:23.938][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-10 19:46:23.940][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-10 19:46:23.942][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-10 19:46:23.944][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-10 19:46:23.946][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-10 19:46:23.948][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-10 19:46:23.950][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-10 19:46:23.952][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-10 19:46:23.953][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-10 19:46:23.955][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-10 19:46:23.957][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-10 19:46:23.959][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-10 19:46:23.961][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-10 19:46:23.962][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-10 19:46:23.964][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-10 19:46:23.966][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-10 19:46:23.968][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-10 19:46:23.970][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-10 19:46:23.971][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-10 19:46:23.972][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-10 19:46:23.973][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-10 19:46:23.975][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-10 19:46:23.976][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-10 19:46:23.978][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-10 19:46:23.980][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-10 19:46:23.982][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-10 19:46:23.983][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-10 19:46:23.985][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-10 19:46:23.987][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-10 19:46:23.988][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-10 19:46:23.990][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-10 19:46:23.992][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-10 19:46:23.994][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-10 19:46:23.995][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-10 19:46:23.997][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-10 19:46:23.998][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-10 19:46:23.999][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-10 19:46:24.000][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-10 19:46:24.002][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-10 19:46:24.004][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-10 19:46:24.006][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-10 19:46:24.007][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-10 19:46:24.009][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-10 19:46:24.011][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-10 19:46:24.012][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-10 19:46:24.014][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-10 19:46:24.016][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-10 19:46:24.018][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-10 19:46:24.020][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-10 19:46:24.022][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-10 19:46:24.023][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-10 19:46:24.025][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-10 19:46:24.026][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-10 19:46:24.027][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-10 19:46:24.028][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-10 19:46:24.030][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-10 19:46:24.032][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-10 19:46:24.033][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-10 19:46:24.035][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-10 19:46:24.037][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-10 19:46:24.038][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-10 19:46:24.040][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-10 19:46:24.041][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-10 19:46:24.043][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-10 19:46:24.045][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-10 19:46:24.046][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-10 19:46:24.048][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-10 19:46:24.050][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-10 19:46:24.052][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-10 19:46:24.054][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-10 19:46:24.056][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-10 19:46:24.058][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-10 19:46:24.060][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-10 19:46:24.062][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-10 19:46:24.063][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-10 19:46:24.065][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-10 19:46:24.067][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-10 19:46:24.068][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-10 19:46:24.070][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-10 19:46:24.071][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-10 19:46:24.073][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-10 19:46:24.076][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-10 19:46:24.077][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 19:46:24.078][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:24.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:24.081][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:24.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:24.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:24.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:24.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:24.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:24.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:24.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:24.090][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[2025-02-10 19:46:24.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:24.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:24.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:24.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:24.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:24.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:24.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:24.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:24.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:24.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:24.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:24.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:24.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:24.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:24.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:24.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:24.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:24.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:24.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:24.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:24.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:24.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:24.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:24.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:24.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:24.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:24.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:24.120][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.DEBUG[2025-02-10 19:46:24.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:24.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:24.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:24.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:24.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:24.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:24.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:24.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:24.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:24.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:24.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:24.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:24.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:24.136][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.DEBUG[2025-02-10 19:46:24.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:24.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:24.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:24.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:24.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:24.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:24.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:24.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:24.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:24.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:24.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:24.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:24.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:24.151][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.DEBUG[2025-02-10 19:46:24.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:24.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:24.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:24.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:24.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:24.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:24.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:24.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:24.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:24.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:24.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:24.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:24.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:24.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:24.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:24.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:24.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:24.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:24.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:24.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:24.176][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[2025-02-10 19:46:24.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:24.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:24.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:24.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:24.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:24.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:24.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:24.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:24.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:24.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:24.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:24.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:24.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:24.192][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[2025-02-10 19:46:24.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:24.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:24.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:24.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:24.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:24.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:24.202][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[2025-02-10 19:46:24.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:24.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:24.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:24.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:24.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:24.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:24.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:24.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 19:46:24.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:24.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:24.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:24.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:24.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:24.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:24.228][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-02-10 19:46:24.230][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-02-10 19:46:24.232][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:24.234][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-10 19:46:24.235][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:24.237][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 19:46:24.238][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:24.239][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 19:46:24.240][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:24.242][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-02-10 19:46:24.243][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-10 19:46:24.244][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 19:46:24.246][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:24.247][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-02-10 19:46:24.249][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 19:46:24.250][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-02-10 19:46:24.250][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-02-10 19:46:24.250][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-02-10 19:46:24.250][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-02-10 19:46:24.250][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-02-10 19:46:24.250][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-02-10 19:46:24.250][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-02-10 19:46:24.250][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-02-10 19:46:24.250][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-02-10 19:46:24.250][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-02-10 19:46:24.250][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-02-10 19:46:24.252][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-10 19:46:24.253][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 19:46:24.253][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 19:46:24.253][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 19:46:24.255][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-10 19:46:24.256][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:24.257][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:24.259][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 19:46:24.260][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 19:46:24.261][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 19:46:24.262][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 19:46:24.264][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:46:24.264][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-02-10 19:46:24.265][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 19:46:24.266][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 19:46:24.267][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-10 19:46:24.269][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-02-10 19:46:24.269][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-02-10 19:46:24.270][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-10 19:46:24.273][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-10 19:46:24.275][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-02-10 19:46:24.277][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-10 19:46:24.279][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-10 19:46:24.281][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-10 19:46:24.286][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-02-10 19:46:24.288][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-02-10 19:46:24.289][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-02-10 19:46:24.291][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-02-10 19:46:24.293][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-10 19:46:24.295][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-10 19:46:24.296][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-02-10 19:46:24.297][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-02-10 19:46:24.299][biodb::testThat]
biodb.INFO [2025-02-10 19:46:24.300][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-02-10 19:46:24.301][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 19:46:24.310][biodb::testThat]
biodb.DEBUG[2025-02-10 19:46:24.315][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-02-10 19:46:24.320][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 19:46:24.322][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-02-10 19:46:24.324][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:46:24.326][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-02-10 19:46:24.330][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-10 19:46:24.335][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 19:46:24.337][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-02-10 19:46:24.339][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 19:46:24.341][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-02-10 19:46:24.348][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-02-10 19:46:24.349][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 19:46:24.352][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-02-10 19:46:24.354][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 19:46:24.355][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 19:46:24.357][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 19:46:24.359][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 19:46:24.360][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 19:46:24.361][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 19:46:24.365][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:24.367][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:24.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:24.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:24.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:24.378][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:24.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 19:46:24.380][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-02-10 19:46:24.383][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 19:46:24.384][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 19:46:24.386][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-02-10 19:46:26.484][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-02-10 19:46:27.587][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 19:46:27.590][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-02-10 19:46:27.595][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-02-10 19:46:27.599][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-02-10 19:46:27.602][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 19:46:27.604][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 19:46:27.605][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 19:46:27.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 19:46:27.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:27.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:27.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:27.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:27.619][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:27.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 19:46:27.626][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:27.627][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:27.628][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.630][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:27.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:27.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.636][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:46:27.638][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:46:27.639][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.640][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.642][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 19:46:27.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 19:46:27.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.647][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:46:27.648][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:46:27.649][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.651][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.652][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 19:46:27.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 19:46:27.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.658][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 19:46:27.659][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 19:46:27.660][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.661][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.663][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 19:46:27.665][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 19:46:27.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.667][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.669][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:46:27.670][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:46:27.671][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.673][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.674][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:46:27.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 19:46:27.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.680][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:46:27.681][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:27.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.684][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.685][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 19:46:27.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 19:46:27.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.691][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:27.692][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:27.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.694][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:27.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 19:46:27.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.701][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:46:27.703][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:46:27.704][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.705][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.707][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 19:46:27.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 19:46:27.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.712][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:46:27.714][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:46:27.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.716][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.718][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 19:46:27.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 19:46:27.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.723][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:46:27.725][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:46:27.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.727][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.729][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 19:46:27.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 19:46:27.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.734][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:27.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:27.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:27.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:27.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:27.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:27.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.750][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 19:46:27.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 19:46:27.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:27.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:27.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:27.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:27.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:27.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:27.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:27.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:27.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:27.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:27.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 19:46:27.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 19:46:27.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 19:46:27.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 19:46:27.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 19:46:27.877][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-02-10 19:46:27.896][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-10 19:46:27.898][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-02-10 19:46:27.899][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-02-10 19:46:27.901][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-10 19:46:27.902][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 19:46:27.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 19:46:27.909][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 19:46:27.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 19:46:27.913][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 19:46:27.914][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
> 
> proc.time()
   user  system elapsed 
 21.777   1.364  63.006

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

name	user	system	elapsed
ChebiConn	2.716	1.106	5.364
ChebiEntry	0.392	0.018	0.443