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This page was generated on 2025-04-17 11:43 -0400 (Thu, 17 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4667
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 206/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-04-16 13:40 -0400 (Wed, 16 Apr 2025)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: RELEASE_3_21
git_last_commit: b8d718f
git_last_commit_date: 2025-04-15 12:39:10 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

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: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.14.0.tar.gz
StartedAt: 2025-04-16 19:53:09 -0400 (Wed, 16 Apr 2025)
EndedAt: 2025-04-16 19:56:06 -0400 (Wed, 16 Apr 2025)
EllapsedTime: 176.6 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbChebi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: 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 ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
ChebiConn 2.765  1.118   5.084
* 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 ‘1.14.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbChebi)

Tests output

biodbChebi.Rcheck/tests/testthat.Rout


R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: 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 [2025-04-16 19:54:11.668][biodb::testContext]
biodb.INFO [2025-04-16 19:54:11.673][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-16 19:54:11.675][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-04-16 19:54:11.676][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-16 19:54:11.677][biodb::testContext]
biodb.INFO [2025-04-16 19:54:11.685][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-16 19:54:11.688][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-16 19:54:11.698][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-16 19:54:11.700][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-16 19:54:11.701][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-16 19:54:11.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:11.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:11.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:11.707][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-16 19:54:11.733][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-16 19:54:11.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:11.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:11.737][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[2025-04-16 19:54:11.738][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-16 19:54:11.739][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-16 19:54:11.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:11.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:11.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:11.744][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-16 19:54:11.746][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-16 19:54:11.747][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-16 19:54:11.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:11.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:11.751][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[2025-04-16 19:54:11.752][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-16 19:54:11.753][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-16 19:54:11.755][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-16 19:54:11.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:11.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:11.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:11.759][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-16 19:54:11.760][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-16 19:54:11.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:11.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:11.764][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[2025-04-16 19:54:11.765][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-16 19:54:11.766][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-16 19:54:11.767][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-16 19:54:11.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:11.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:11.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:11.772][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-16 19:54:11.773][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-16 19:54:11.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:11.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:11.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:11.777][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-16 19:54:11.778][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-16 19:54:11.780][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-16 19:54:11.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:11.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:11.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:11.783][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-16 19:54:11.784][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-16 19:54:11.785][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-16 19:54:11.786][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-16 19:54:11.787][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-16 19:54:11.788][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-16 19:54:11.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:11.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:11.792][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[2025-04-16 19:54:11.793][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-16 19:54:11.794][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-16 19:54:11.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:11.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:11.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:11.799][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-16 19:54:11.800][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-16 19:54:11.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:11.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:11.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:11.805][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-16 19:54:11.807][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-16 19:54:11.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:11.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:11.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:11.812][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-16 19:54:11.813][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-16 19:54:11.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:11.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:11.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:11.818][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-16 19:54:11.819][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-16 19:54:11.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:11.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:11.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:11.823][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-16 19:54:11.825][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-16 19:54:11.852][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-16 19:54:11.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:11.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:11.857][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[2025-04-16 19:54:11.858][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-16 19:54:11.859][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-16 19:54:11.860][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-16 19:54:11.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:11.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:11.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:11.868][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-16 19:54:11.913][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-16 19:54:11.942][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-16 19:54:11.943][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-16 19:54:11.944][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-16 19:54:11.946][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-16 19:54:11.947][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-16 19:54:11.948][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-16 19:54:11.950][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-16 19:54:11.951][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-16 19:54:11.952][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-16 19:54:11.954][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-16 19:54:11.955][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-16 19:54:11.956][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-16 19:54:11.957][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:54:11.958][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-16 19:54:11.959][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-16 19:54:11.959][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-16 19:54:11.959][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-16 19:54:11.959][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-16 19:54:11.959][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-16 19:54:11.961][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-16 19:54:11.962][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:54:11.963][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:54:11.965][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-16 19:54:11.966][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:54:11.967][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:54:11.968][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-16 19:54:11.970][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:54:11.971][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-16 19:54:11.972][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-16 19:54:11.973][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-16 19:54:11.975][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:54:11.976][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-16 19:54:11.979][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-16 19:54:11.980][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-16 19:54:11.982][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-16 19:54:11.983][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-16 19:54:11.984][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-16 19:54:11.986][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-16 19:54:11.987][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-16 19:54:11.989][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-16 19:54:11.990][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-16 19:54:11.992][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-16 19:54:11.992][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-16 19:54:11.994][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-16 19:54:11.995][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-16 19:54:11.996][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:54:11.997][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-16 19:54:11.998][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-16 19:54:11.998][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-16 19:54:11.998][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-16 19:54:11.998][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-16 19:54:11.998][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-16 19:54:11.999][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-16 19:54:12.000][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:54:12.002][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:54:12.003][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-16 19:54:12.004][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:54:12.005][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:54:12.007][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-16 19:54:12.008][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:54:12.009][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-16 19:54:12.010][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-16 19:54:12.011][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-16 19:54:12.013][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:54:12.014][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-16 19:54:12.016][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-16 19:54:12.017][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-16 19:54:12.019][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-16 19:54:12.020][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-16 19:54:12.021][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-16 19:54:12.022][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-16 19:54:12.024][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-16 19:54:12.025][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-16 19:54:12.026][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-16 19:54:12.028][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-16 19:54:12.029][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-16 19:54:12.030][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-16 19:54:12.031][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-16 19:54:12.033][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:54:12.034][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-16 19:54:12.035][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:54:12.036][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-16 19:54:12.037][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:54:12.038][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:54:12.039][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-16 19:54:12.040][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:54:12.041][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:54:12.042][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-16 19:54:12.043][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:54:12.044][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-16 19:54:12.045][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-16 19:54:12.047][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-16 19:54:12.047][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:54:12.049][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-16 19:54:12.051][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-16 19:54:12.052][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-16 19:54:12.053][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-16 19:54:12.054][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-16 19:54:12.055][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-16 19:54:12.056][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-16 19:54:12.058][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-16 19:54:12.059][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-16 19:54:12.060][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-16 19:54:12.061][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-16 19:54:12.062][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-16 19:54:12.064][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-16 19:54:12.065][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-16 19:54:12.066][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:54:12.067][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-16 19:54:12.068][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:54:12.069][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-16 19:54:12.070][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:54:12.072][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:54:12.073][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-16 19:54:12.074][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:54:12.075][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:54:12.075][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-16 19:54:12.077][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:54:12.078][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-16 19:54:12.079][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-16 19:54:12.080][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-16 19:54:12.081][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:54:12.087][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-16 19:54:12.088][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.143][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[2025-04-16 19:54:12.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.160][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[2025-04-16 19:54:12.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.187][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-16 19:54:12.193][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-16 19:54:12.195][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-16 19:54:12.197][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-16 19:54:12.199][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-16 19:54:12.201][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-16 19:54:12.202][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-16 19:54:12.204][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-16 19:54:12.206][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-16 19:54:12.208][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-16 19:54:12.210][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-16 19:54:12.211][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-16 19:54:12.213][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-16 19:54:12.215][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-16 19:54:12.216][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-16 19:54:12.218][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-16 19:54:12.220][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-16 19:54:12.221][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-16 19:54:12.223][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-16 19:54:12.225][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-16 19:54:12.226][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-16 19:54:12.227][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-16 19:54:12.229][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-16 19:54:12.230][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-16 19:54:12.232][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-16 19:54:12.234][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-16 19:54:12.235][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-16 19:54:12.236][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-16 19:54:12.238][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-16 19:54:12.240][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-16 19:54:12.241][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-16 19:54:12.243][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-16 19:54:12.245][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-16 19:54:12.247][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-16 19:54:12.248][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-16 19:54:12.250][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-16 19:54:12.251][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-16 19:54:12.252][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-16 19:54:12.254][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-16 19:54:12.255][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-16 19:54:12.257][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-16 19:54:12.259][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-16 19:54:12.260][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-16 19:54:12.261][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-16 19:54:12.263][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-16 19:54:12.264][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-16 19:54:12.266][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-16 19:54:12.268][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-16 19:54:12.269][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-16 19:54:12.271][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-16 19:54:12.273][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-16 19:54:12.274][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-16 19:54:12.275][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-16 19:54:12.277][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-16 19:54:12.279][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-16 19:54:12.281][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-16 19:54:12.282][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-16 19:54:12.284][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-16 19:54:12.285][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-16 19:54:12.287][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-16 19:54:12.289][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-16 19:54:12.291][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-16 19:54:12.292][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-16 19:54:12.293][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-16 19:54:12.295][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-16 19:54:12.297][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-16 19:54:12.299][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-16 19:54:12.300][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-16 19:54:12.302][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-16 19:54:12.304][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-16 19:54:12.306][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-16 19:54:12.307][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-16 19:54:12.309][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-16 19:54:12.310][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-16 19:54:12.312][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-16 19:54:12.313][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-16 19:54:12.315][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-16 19:54:12.316][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-16 19:54:12.318][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-16 19:54:12.319][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-16 19:54:12.321][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-16 19:54:12.323][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-16 19:54:12.324][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-16 19:54:12.331][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-16 19:54:12.333][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-16 19:54:12.337][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-16 19:54:12.338][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.340][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:12.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:12.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:12.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:12.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:12.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:12.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:12.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:12.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:12.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:12.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:12.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:12.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:12.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:12.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.404][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.DEBUG[2025-04-16 19:54:12.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:12.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:12.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:12.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:12.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:12.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:12.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:12.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:12.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:12.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:12.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:12.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:12.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:12.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:12.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:12.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:12.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:12.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:12.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:12.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:54:12.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:12.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:12.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.482][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[2025-04-16 19:54:12.485][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-16 19:54:12.497][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-16 19:54:12.500][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-16 19:54:12.502][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-16 19:54:12.503][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-16 19:54:12.504][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-16 19:54:12.505][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-16 19:54:12.506][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-16 19:54:12.508][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-16 19:54:12.509][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-16 19:54:12.510][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-16 19:54:12.511][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-16 19:54:12.512][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-16 19:54:12.513][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-16 19:54:12.515][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-16 19:54:12.516][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-16 19:54:12.516][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-16 19:54:12.516][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-16 19:54:12.516][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-16 19:54:12.516][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-16 19:54:12.516][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-16 19:54:12.516][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-16 19:54:12.516][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-16 19:54:12.516][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-16 19:54:12.516][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-16 19:54:12.516][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-16 19:54:12.518][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-16 19:54:12.519][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-16 19:54:12.519][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-16 19:54:12.519][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-16 19:54:12.520][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-16 19:54:12.521][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:54:12.522][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:54:12.524][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-16 19:54:12.525][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:54:12.526][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:54:12.528][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-16 19:54:12.529][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:12.529][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-16 19:54:12.530][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-16 19:54:12.531][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-16 19:54:12.533][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-16 19:54:12.534][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-16 19:54:12.534][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-16 19:54:12.542][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-16 19:54:12.545][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-16 19:54:12.547][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-16 19:54:12.549][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-16 19:54:12.551][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-16 19:54:12.553][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-16 19:54:12.581][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-16 19:54:12.583][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-16 19:54:12.587][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-16 19:54:12.592][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-16 19:54:12.635][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-16 19:54:12.636][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-16 19:54:12.638][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-16 19:54:12.640][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-16 19:54:12.651][biodb::testThat]
biodb.INFO [2025-04-16 19:54:12.652][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-04-16 19:54:12.654][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:54:12.655][biodb::testThat]
biodb.TRACE[2025-04-16 19:54:12.660][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[2025-04-16 19:54:12.662][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:12.666][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:12.675][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:12.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:12.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:12.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:12.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:12.698][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:12.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:12.710][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:12.712][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:12.713][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.715][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:12.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:12.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.739][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:12.741][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:12.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.743][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.779][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:12.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:12.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.785][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:12.787][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:12.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.789][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.791][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:12.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:12.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.796][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:12.798][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:12.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.800][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.802][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:12.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:12.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.807][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:12.808][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:12.809][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.810][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.812][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:12.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:12.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.817][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:12.819][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:12.820][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.821][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.823][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:12.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:12.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.828][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:12.829][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:12.831][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.832][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.833][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:12.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:12.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.838][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:12.839][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:12.841][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.842][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:12.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:12.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.849][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:12.850][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:12.851][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.853][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.865][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:12.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:12.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.870][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:12.872][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:12.873][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.874][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.876][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:12.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:12.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.881][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:12.882][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:12.883][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.884][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.885][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:12.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:12.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:12.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:12.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:12.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:12.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:12.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:12.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:12.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:12.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:12.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:12.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:12.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:12.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:12.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:12.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:12.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:12.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:12.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:12.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:12.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:12.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:12.983][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-04-16 19:54:12.987][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:12.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:12.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:12.993][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:12.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:12.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:12.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.029][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:13.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:13.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.041][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:13.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:13.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.046][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:13.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:13.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:13.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:13.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.054][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-16 19:54:13.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-16 19:54:13.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.058][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-16 19:54:13.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-16 19:54:13.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.062][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-16 19:54:13.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-16 19:54:13.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.067][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-16 19:54:13.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-16 19:54:13.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:13.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:13.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.114][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:13.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:13.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:13.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:13.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:13.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:13.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:13.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:13.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:13.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:13.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:13.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:13.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:13.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:13.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.159][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:13.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:13.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:13.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:13.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:13.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:13.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:13.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:13.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:13.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:13.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:13.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:13.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.197][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:13.198][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:13.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.201][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:13.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:13.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:13.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:13.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:13.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:13.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:13.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:13.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.242][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:13.243][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:13.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.246][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:13.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:13.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.262][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:13.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:13.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.267][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:13.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:13.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.273][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:13.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:13.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.278][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:13.279][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:13.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.282][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.283][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:13.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:13.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.301][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:13.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:13.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.307][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:13.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:13.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.312][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:13.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:13.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.330][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:13.331][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:13.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.334][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.335][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:13.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:13.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.353][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:13.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:13.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:13.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:13.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:13.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:13.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.370][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:13.371][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:13.372][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.374][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:13.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:13.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:13.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:13.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.397][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:13.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:13.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:13.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:13.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.409][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:13.410][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:13.411][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.413][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:13.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:13.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.431][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:13.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:13.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.437][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:13.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:13.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.443][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:13.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:13.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.448][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:13.449][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:13.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.457][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.459][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:13.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:13.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.475][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-16 19:54:13.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:13.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.481][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-16 19:54:13.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:13.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.486][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-16 19:54:13.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:13.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.491][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-16 19:54:13.492][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:13.493][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.495][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.496][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-16 19:54:13.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:13.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.511][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:13.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:13.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.517][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:13.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:13.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.522][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:13.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:13.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.525][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:13.527][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:13.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.529][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.530][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:13.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:13.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.546][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:13.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:13.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.552][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:13.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:13.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.557][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:13.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:13.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.561][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:13.562][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:13.564][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.565][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.566][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:13.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:13.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.582][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:13.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:13.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.588][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:13.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:13.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.594][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:13.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:13.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.600][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:13.601][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:13.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.603][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.604][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:13.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:13.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.618][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:13.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:13.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.624][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:13.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:13.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.628][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:13.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:13.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.633][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:13.634][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:13.635][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.637][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.638][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:13.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:13.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.660][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:13.662][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:13.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.664][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.671][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:13.672][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:13.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.675][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.682][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:13.683][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:13.685][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.686][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.693][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:13.695][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:13.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.698][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.705][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:13.707][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:13.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.710][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.717][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:13.719][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:13.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.722][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.729][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:13.731][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:13.732][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.733][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.740][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:13.742][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:13.743][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.744][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.751][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-16 19:54:13.752][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:13.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.755][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.762][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:13.763][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:13.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.766][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.773][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:13.775][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:13.776][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.778][ef$get] fields variable is a list.
biodb.INFO [2025-04-16 19:54:13.790][biodb::testThat]
biodb.INFO [2025-04-16 19:54:13.791][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-04-16 19:54:13.793][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:54:13.794][biodb::testThat]
biodb.DEBUG[2025-04-16 19:54:13.811][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-04-16 19:54:13.819][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:13.824][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-04-16 19:54:13.826][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-16 19:54:13.828][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-04-16 19:54:13.830][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:13.872][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:13.873][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:13.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:13.877][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:13.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:13.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:13.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:13.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:13.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:13.892][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:13.893][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:13.894][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.895][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:13.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:13.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.925][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:13.927][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:13.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.929][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.931][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:13.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:13.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.936][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:13.938][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:13.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.940][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.941][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:13.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:13.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.946][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:13.947][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:13.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.950][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.951][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:13.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:13.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.955][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:13.957][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:13.958][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.959][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.961][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:13.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:13.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.966][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:13.967][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:13.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.969][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.970][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:13.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:13.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.975][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:13.976][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:13.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.978][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.980][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:13.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:13.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.985][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:13.987][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:13.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.989][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:13.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:13.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:13.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:13.996][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:13.998][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:13.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.000][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:14.002][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:14.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:14.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:14.008][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:14.009][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:14.010][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.011][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:14.012][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:14.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:14.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:14.016][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:14.018][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:14.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.020][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:14.022][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:14.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:14.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:14.026][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:14.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:14.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:14.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:14.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:14.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:14.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:14.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:14.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:14.046][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:14.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:14.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:14.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:14.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:14.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:14.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:14.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:14.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:14.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:14.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:14.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:14.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:14.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:14.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:14.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:14.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:14.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:14.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:14.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:14.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:14.079][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-04-16 19:54:14.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-16 19:54:14.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-16 19:54:14.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:14.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-16 19:54:14.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-16 19:54:14.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:14.090][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-16 19:54:14.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-16 19:54:14.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-16 19:54:14.105][biodb::testThat]
biodb.INFO [2025-04-16 19:54:14.107][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-04-16 19:54:14.108][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:54:14.109][biodb::testThat]
biodb.TRACE[2025-04-16 19:54:14.113][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:14.115][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:14.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.117][ef$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:14.119][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-04-16 19:54:14.150][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:14.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:14.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:14.155][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:14.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:14.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:14.161][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:14.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:14.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:14.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:14.172][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-04-16 19:54:14.177][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-16 19:54:14.202][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-16 19:54:14.229][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-04-16 19:54:14.231][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-16 19:54:14.234][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-04-16 19:54:14.260][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:54:14.266][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:14.267][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:14.268][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-16 19:54:15.864][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-16 19:54:16.524][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:16.527][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-04-16 19:54:16.543][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-04-16 19:54:16.546][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-04-16 19:54:16.563][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:16.564][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:16.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.566][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:16.567][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:16.568][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:16.569][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.570][ef$get] fields variable is a list.
biodb.INFO [2025-04-16 19:54:16.576][biodb::testThat]
biodb.INFO [2025-04-16 19:54:16.577][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-04-16 19:54:16.579][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:54:16.580][biodb::testThat]
biodb.TRACE[2025-04-16 19:54:16.615][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:16.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:16.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:16.621][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:16.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:16.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:16.638][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:16.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:16.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:16.712][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:54:16.717][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-16 19:54:16.718][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-16 19:54:16.720][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-16 19:54:16.722][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-04-16 19:54:16.748][biodb::testThat]
biodb.INFO [2025-04-16 19:54:16.750][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-04-16 19:54:16.751][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:54:16.752][biodb::testThat]
biodb.TRACE[2025-04-16 19:54:16.785][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:16.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:16.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:16.795][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:16.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:16.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:16.801][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:16.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:16.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:16.807][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:16.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:16.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:16.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:16.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:16.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:16.818][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:16.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:16.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:16.824][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-16 19:54:16.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-16 19:54:16.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:16.830][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-16 19:54:16.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-16 19:54:16.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:16.836][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-16 19:54:16.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-16 19:54:16.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:16.842][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-16 19:54:16.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-16 19:54:16.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:16.874][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:16.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:16.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:16.880][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:16.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:16.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:16.886][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:16.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:16.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:16.891][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:16.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:16.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:16.896][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:16.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:16.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:16.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:16.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:16.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:16.906][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-16 19:54:16.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-16 19:54:16.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:16.912][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-16 19:54:16.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-16 19:54:16.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:16.917][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-16 19:54:16.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-16 19:54:16.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:16.930][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-16 19:54:16.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-16 19:54:16.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:16.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-16 19:54:16.945][biodb::testThat]
biodb.INFO [2025-04-16 19:54:16.946][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-04-16 19:54:16.948][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:54:16.949][biodb::testThat]
biodb.INFO [2025-04-16 19:54:16.962][biodb::testThat]
biodb.INFO [2025-04-16 19:54:16.964][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-04-16 19:54:16.965][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:54:16.967][biodb::testThat]
biodb.INFO [2025-04-16 19:54:16.979][biodb::testThat]
biodb.INFO [2025-04-16 19:54:16.980][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-04-16 19:54:16.982][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:54:16.983][biodb::testThat]
biodb.DEBUG[2025-04-16 19:54:16.988][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-04-16 19:54:18.106][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-04-16 19:54:19.132][biodb::testThat]
biodb.INFO [2025-04-16 19:54:19.133][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-04-16 19:54:19.134][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:54:19.136][biodb::testThat]
biodb.DEBUG[2025-04-16 19:54:19.488][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2025-04-16 19:54:19.892][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:19.894][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:19.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:19.897][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:19.898][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:19.900][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:19.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:19.902][ef$get] fields variable is a list.
biodb.INFO [2025-04-16 19:54:19.905][biodb::testThat]
biodb.INFO [2025-04-16 19:54:19.906][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-04-16 19:54:19.907][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:54:19.909][biodb::testThat]
biodb.TRACE[2025-04-16 19:54:19.927][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:19.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:19.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:19.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:19.933][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:19.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:19.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:19.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:19.939][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:19.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:19.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:19.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:20.065][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:54:20.070][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-16 19:54:20.072][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-16 19:54:20.074][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-16 19:54:20.076][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-16 19:54:20.174][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:54:20.179][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-16 19:54:20.181][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-16 19:54:20.183][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-16 19:54:20.185][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-04-16 19:54:20.210][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-16 19:54:20.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-16 19:54:20.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:20.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:20.224][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:20.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:20.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:20.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:20.230][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:20.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:20.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:20.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:20.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:20.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:20.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:20.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:20.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:20.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:20.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:20.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:20.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:20.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:20.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:20.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:20.262][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:54:20.292][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:20.294][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:20.315][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-16 19:54:20.920][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-16 19:54:21.260][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:21.263][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-04-16 19:54:21.269][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-04-16 19:54:21.273][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:21.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:21.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:21.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:21.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:21.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:21.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:21.288][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-04-16 19:54:21.364][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:21.367][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-04-16 19:54:21.369][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:21.370][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:21.372][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:21.374][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:21.375][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:21.377][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:21.380][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:21.382][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:21.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:21.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:21.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:21.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:21.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:21.396][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-04-16 19:54:21.400][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:21.401][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:21.403][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-04-16 19:54:21.767][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-04-16 19:54:22.104][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:22.107][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-04-16 19:54:22.113][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-04-16 19:54:22.117][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-04-16 19:54:22.119][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:22.121][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:22.122][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:22.125][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:22.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:22.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:22.134][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:22.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:22.137][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:22.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:22.142][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:22.143][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:22.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.146][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:22.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:22.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.153][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:22.154][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:22.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.157][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.158][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:22.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:22.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.164][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:22.165][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:22.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.175][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.181][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:22.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:22.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.188][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:22.190][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:22.191][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.192][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.194][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:22.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:22.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.200][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:22.202][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:22.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.205][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.206][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:22.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:22.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.212][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:22.214][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:22.215][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.216][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.218][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:22.220][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:22.221][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.223][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.224][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:22.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:22.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.230][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:22.232][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:22.233][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.235][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.236][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:22.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:22.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.242][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:22.243][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:22.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.246][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.248][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:22.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:22.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.253][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:22.255][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:22.256][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.258][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.259][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:22.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:22.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.265][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:22.266][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:22.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.269][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.271][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:22.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:22.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.276][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:22.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:22.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:22.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:22.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:22.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:22.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:22.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:22.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:22.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:22.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:22.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:22.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:22.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:22.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:22.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:22.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:22.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:22.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:22.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:22.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:22.338][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-04-16 19:54:22.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:22.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:22.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.358][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:22.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:22.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:22.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:22.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:22.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:22.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:22.370][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:54:22.375][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:22.377][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:22.380][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-16 19:54:22.716][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-16 19:54:23.959][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:23.962][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-04-16 19:54:23.968][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-04-16 19:54:23.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:23.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:23.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:24.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:24.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:24.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:24.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:24.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:24.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:24.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:24.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:24.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.018][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:24.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:24.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:24.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:24.036][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:24.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:24.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:24.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:24.047][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:24.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:24.050][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-04-16 19:54:24.051][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:24.053][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-04-16 19:54:24.056][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:24.057][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:24.059][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:24.060][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:24.061][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:24.062][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:24.081][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:24.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:24.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:24.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:24.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:24.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:24.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:24.097][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-04-16 19:54:24.101][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:24.102][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:24.104][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-04-16 19:54:24.463][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-04-16 19:54:24.805][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:24.808][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-04-16 19:54:24.813][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-04-16 19:54:24.818][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-04-16 19:54:24.821][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:24.822][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:24.824][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:24.826][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:24.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:24.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:24.835][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:24.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:24.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:24.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:24.842][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:24.843][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:24.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.845][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:24.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:24.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.852][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:24.853][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:24.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.855][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.857][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:24.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:24.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.861][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:24.872][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:24.874][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.875][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.877][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:24.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:24.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.882][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:24.883][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:24.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.885][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.887][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:24.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:24.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.891][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:24.892][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:24.893][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.894][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.895][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:24.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:24.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.900][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:24.902][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:24.903][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.904][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.906][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:24.907][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:24.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.909][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.911][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:24.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:24.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.916][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:24.918][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:24.919][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.920][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.922][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:24.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:24.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.927][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:24.929][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:24.930][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.931][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.933][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:24.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:24.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.939][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:24.940][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:24.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.942][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.944][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:24.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:24.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.950][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:24.952][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:24.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.954][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.956][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:24.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:24.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:24.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:24.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:24.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:24.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:24.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:24.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:24.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:24.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:24.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:24.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:24.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:24.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:24.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:24.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:25.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:25.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:25.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:25.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:25.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:25.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:25.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:25.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:25.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:25.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:25.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:25.047][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-04-16 19:54:25.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:25.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:25.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:25.054][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:25.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:25.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:25.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:25.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:25.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:25.091][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:54:25.096][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-16 19:54:25.098][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-16 19:54:25.100][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-16 19:54:25.101][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-16 19:54:25.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:25.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:25.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:25.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:25.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:25.117][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:25.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:25.119][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:25.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:25.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:25.124][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:25.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:25.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:25.143][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:25.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:25.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:25.148][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:25.149][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:25.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:25.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:25.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:25.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:25.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:25.163][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-04-16 19:54:25.165][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:25.166][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-04-16 19:54:25.168][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:25.169][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:25.171][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:25.172][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:25.174][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:25.175][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:25.179][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:25.186][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:25.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:25.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:25.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:25.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:25.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:25.200][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-04-16 19:54:25.203][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:25.205][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:25.206][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-04-16 19:54:25.551][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-04-16 19:54:25.891][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:25.894][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-04-16 19:54:25.899][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-04-16 19:54:25.902][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-04-16 19:54:25.904][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:25.906][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:25.908][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:25.909][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:25.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:25.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:25.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:25.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:25.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:25.922][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.TRACE[2025-04-16 19:54:25.924][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:25.925][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:25.926][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.927][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:25.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:25.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:25.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:25.934][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:25.935][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:25.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.937][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:25.938][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:25.939][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:25.940][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.941][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:25.943][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:25.944][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:25.945][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.946][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:25.948][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:25.949][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:25.950][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.951][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:25.953][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:25.954][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:25.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.956][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:25.957][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:25.958][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:25.959][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.960][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:25.962][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:25.963][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:25.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.965][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:25.967][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:25.968][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:25.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.971][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:25.973][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:25.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:25.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:25.978][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:25.979][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:25.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.982][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:25.983][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:25.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:25.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:25.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:25.988][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:25.989][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:25.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.002][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:26.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:26.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:26.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:26.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:26.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:26.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:26.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:26.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:26.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:26.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:26.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:26.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:26.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:26.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:26.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:26.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:26.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:26.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:26.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:26.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:26.058][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-04-16 19:54:26.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:26.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:26.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:26.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:26.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:26.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:26.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:26.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:26.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:26.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:26.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:26.099][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:26.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:26.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:26.110][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:26.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:26.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:26.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:26.117][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-04-16 19:54:26.119][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:26.121][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-04-16 19:54:26.122][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:26.124][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:26.125][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:26.127][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:26.128][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:26.130][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:26.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:26.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:26.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:26.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:26.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:26.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:26.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:26.149][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-04-16 19:54:26.161][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:26.163][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:26.166][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-04-16 19:54:26.517][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-04-16 19:54:26.853][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:26.855][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-04-16 19:54:26.860][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-04-16 19:54:26.864][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-04-16 19:54:26.867][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:26.868][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:26.870][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:26.872][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:26.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:26.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:26.882][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:26.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:26.884][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:26.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:26.889][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:26.890][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:26.891][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.893][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:26.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:26.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.899][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:26.900][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:26.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.903][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.905][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:26.907][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:26.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.909][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.911][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:26.913][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:26.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.915][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.917][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:26.918][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:26.919][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.921][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.922][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:26.923][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:26.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.926][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.928][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:26.929][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:26.930][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.932][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.933][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:26.935][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:26.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.937][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.939][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:26.940][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:26.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.943][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:26.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:26.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.951][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:26.952][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:26.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.955][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.956][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:26.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:26.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.961][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:26.963][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:26.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.965][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:26.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:26.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:26.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:26.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:26.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:26.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:26.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:27.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:27.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:27.010][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:27.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:27.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:27.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:27.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:27.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:27.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:27.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:27.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:27.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:27.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:27.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:27.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:27.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:27.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:27.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:27.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:27.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:27.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:27.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:27.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:27.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:27.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:27.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:27.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:27.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:27.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:27.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:27.050][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-04-16 19:54:27.051][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:27.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:27.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:27.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:27.057][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:27.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:27.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:27.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:27.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:27.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:27.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:27.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:27.069][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:27.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:27.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:27.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:27.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:27.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:27.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:27.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:27.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:27.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:27.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:27.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:27.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:27.091][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:27.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:27.094][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-04-16 19:54:27.095][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:27.097][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-04-16 19:54:27.099][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:27.100][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:27.101][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:27.103][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:27.104][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:27.105][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:27.108][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:27.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:27.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:27.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:27.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:27.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:27.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:27.123][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-04-16 19:54:27.126][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:27.128][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:27.129][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-04-16 19:54:27.587][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-04-16 19:54:27.931][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:27.933][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-04-16 19:54:27.950][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-04-16 19:54:27.954][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-04-16 19:54:27.957][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:27.958][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:27.960][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:27.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:27.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:27.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:27.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:27.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:27.976][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:27.977][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[2025-04-16 19:54:27.980][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:27.982][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:27.983][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:27.985][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:27.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:27.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:27.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:27.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:27.992][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:27.993][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:27.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:27.995][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:27.997][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:27.998][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:27.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.001][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.003][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:28.004][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:28.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.007][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.008][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:28.010][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:28.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.012][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.013][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:28.015][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:28.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.017][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.018][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:28.020][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:28.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.022][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.023][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:28.025][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:28.026][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.027][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.029][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:28.031][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:28.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.033][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.035][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:28.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:28.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.040][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:28.042][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:28.043][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.045][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.046][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:28.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:28.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.052][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:28.054][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:28.055][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.056][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:28.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:28.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:28.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:28.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:28.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:28.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:28.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:28.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:28.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:28.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:28.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:28.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:28.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:28.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:28.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:28.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:28.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:28.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:28.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:28.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:28.114][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-04-16 19:54:28.116][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:28.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:28.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.120][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:28.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:28.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:28.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:28.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.130][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:28.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:28.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.135][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:28.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:28.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:28.140][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:28.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:28.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:28.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:28.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:28.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:28.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:28.154][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-04-16 19:54:28.156][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:28.158][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-04-16 19:54:28.160][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:28.161][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:28.163][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:28.164][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:28.165][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:28.166][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:28.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:28.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:28.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:28.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:28.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:28.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:28.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:28.183][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-04-16 19:54:28.187][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:28.189][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:28.191][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-04-16 19:54:28.526][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-04-16 19:54:28.887][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:28.889][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-04-16 19:54:28.894][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-04-16 19:54:28.898][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-04-16 19:54:28.900][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:28.902][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:28.904][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:28.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:28.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:28.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:28.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:28.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:28.929][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:28.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:28.934][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:28.935][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:28.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.938][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:28.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:28.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.945][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:28.946][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:28.947][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.948][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.950][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:28.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:28.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.955][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:28.956][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:28.958][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.959][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.961][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:28.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:28.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.967][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:28.968][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:28.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.971][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.972][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:28.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:28.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.978][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:28.979][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:28.980][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.982][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.983][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:28.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:28.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.988][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:28.990][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:28.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.992][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.994][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:28.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:28.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:28.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:28.999][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:29.000][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:29.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.002][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.004][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:29.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:29.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.009][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:29.011][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:29.012][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.013][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:29.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:29.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.019][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:29.021][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:29.022][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.023][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.025][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:29.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:29.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.030][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:29.032][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:29.033][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.033][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.035][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:29.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:29.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.040][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:29.042][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:29.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.052][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.054][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:29.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:29.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:29.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:29.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:29.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:29.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:29.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:29.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:29.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:29.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:29.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:29.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:29.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:29.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:29.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:29.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:29.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:29.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:29.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:29.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:29.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:29.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:29.111][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-04-16 19:54:29.112][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:29.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:29.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.117][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:29.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:29.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:29.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:29.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:29.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:29.128][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:29.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:29.138][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:29.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:29.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:29.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:29.144][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-04-16 19:54:29.145][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:29.147][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-04-16 19:54:29.149][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:29.151][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:29.152][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:29.153][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:29.155][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:29.156][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:29.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:29.161][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:29.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:29.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:29.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:29.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:29.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:29.175][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-04-16 19:54:29.178][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:29.180][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:29.189][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-04-16 19:54:29.539][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-04-16 19:54:29.882][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:29.885][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-04-16 19:54:29.890][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-04-16 19:54:29.893][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-04-16 19:54:29.895][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:29.897][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:29.898][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:29.901][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:29.902][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:29.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:29.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:29.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:29.913][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:29.914][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[2025-04-16 19:54:29.917][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:29.919][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:29.920][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.921][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:29.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:29.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.927][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:29.929][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:29.930][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.931][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.932][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:29.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:29.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.938][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:29.940][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:29.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.942][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.944][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:29.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:29.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.950][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:29.951][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:29.952][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.954][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.955][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:29.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:29.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.961][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:29.962][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:29.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.964][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.966][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:29.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:29.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.971][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:29.973][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:29.974][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.976][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.977][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:29.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:29.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.983][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:29.984][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:29.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.987][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.988][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:29.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:29.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:29.994][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:29.996][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:29.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:29.998][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:30.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:30.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:30.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:30.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:30.005][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:30.006][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:30.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:30.015][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:30.021][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:30.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:30.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:30.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:30.028][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:30.029][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:30.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:30.032][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:30.034][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:30.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:30.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:30.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:30.039][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:30.040][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:30.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:30.043][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:30.045][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:30.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:30.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:30.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:30.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:30.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:30.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:30.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:30.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:30.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:30.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:30.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:30.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:30.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:30.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:30.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:30.065][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:30.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:30.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:30.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:30.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:30.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:30.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:30.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:30.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:30.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:30.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:30.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:30.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:30.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:30.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:30.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:30.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:30.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:30.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:30.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:30.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:30.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:30.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:30.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:30.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:30.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:30.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:30.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:30.100][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-04-16 19:54:30.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:30.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:30.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:30.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:30.107][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:30.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:30.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:30.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:30.112][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:30.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:30.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:30.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:30.117][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:30.118][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:30.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:30.127][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:30.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:30.129][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:30.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:30.132][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-04-16 19:54:30.133][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:30.136][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-04-16 19:54:30.137][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:30.139][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:30.140][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:30.142][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:30.143][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:30.157][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:30.168][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:30.170][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:30.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:30.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:30.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:30.184][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:30.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:30.187][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-04-16 19:54:30.190][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:30.192][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:30.193][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-04-16 19:54:30.711][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-04-16 19:54:31.054][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:31.057][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-04-16 19:54:31.062][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-04-16 19:54:31.066][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-04-16 19:54:31.068][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:31.070][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:31.072][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:31.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:31.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:31.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:31.084][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:31.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:31.087][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:31.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:31.091][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:31.092][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:31.094][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.095][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:31.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:31.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.102][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:31.103][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:31.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.106][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.107][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:31.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:31.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.113][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:31.114][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:31.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.117][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.119][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:31.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:31.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.124][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:31.125][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:31.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.128][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.130][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:31.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:31.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.136][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:31.137][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:31.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.140][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.141][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:31.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:31.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.147][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:31.148][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:31.149][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.151][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.152][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:31.154][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:31.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.156][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.158][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:31.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:31.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.175][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:31.176][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:31.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.179][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:31.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:31.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.186][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:31.188][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:31.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.190][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.192][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:31.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:31.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.198][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:31.199][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:31.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.201][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.203][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:31.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:31.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.209][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:31.210][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:31.211][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.212][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.214][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:31.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:31.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:31.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:31.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:31.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:31.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:31.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:31.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:31.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:31.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:31.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:31.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:31.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:31.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:31.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:31.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:31.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:31.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:31.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:31.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:31.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:31.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:31.273][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-04-16 19:54:31.274][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:31.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:31.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:31.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:31.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:31.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:31.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:31.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:31.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:31.291][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:31.292][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:31.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:31.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:31.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:31.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:31.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:31.314][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-04-16 19:54:31.315][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:31.317][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-04-16 19:54:31.319][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:31.320][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:31.322][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:31.323][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:31.324][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:31.325][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:31.328][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:31.329][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:31.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:31.338][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:31.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:31.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:31.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:31.343][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-04-16 19:54:31.346][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:31.348][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:31.350][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-04-16 19:54:31.684][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-04-16 19:54:32.028][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:32.030][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-04-16 19:54:32.034][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-04-16 19:54:32.037][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-04-16 19:54:32.040][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:32.042][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:32.043][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:32.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:32.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:32.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:32.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:32.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:32.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:32.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:32.064][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:32.065][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:32.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.068][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:32.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:32.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.075][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:32.076][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:32.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.079][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.080][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:32.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:32.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.085][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:32.086][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:32.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.088][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.089][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:32.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:32.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.094][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:32.095][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:32.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.098][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.099][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:32.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:32.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.104][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:32.105][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:32.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.107][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.108][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:32.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:32.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.124][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:32.126][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:32.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.128][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.130][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:32.131][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:32.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.134][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.135][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:32.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:32.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.140][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:32.141][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:32.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.143][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:32.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:32.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.149][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:32.150][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:32.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.151][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.153][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:32.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:32.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.158][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:32.159][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:32.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.161][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.163][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:32.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:32.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.168][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:32.169][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:32.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.171][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.173][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:32.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:32.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:32.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:32.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:32.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:32.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:32.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:32.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:32.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:32.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:32.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:32.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:32.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:32.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:32.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:32.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:32.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:32.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:32.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:32.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:32.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:32.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:32.224][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-04-16 19:54:32.226][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:32.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:32.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.231][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:32.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:32.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:32.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:32.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:32.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:32.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:32.245][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:32.246][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:32.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:32.253][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:32.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:32.256][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:32.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:32.258][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-04-16 19:54:32.259][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:32.261][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-04-16 19:54:32.263][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:32.264][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:32.265][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:32.267][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:32.269][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:32.270][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:32.274][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:32.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:32.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:32.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:32.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:32.285][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:32.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:32.288][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-04-16 19:54:32.291][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:32.292][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:32.294][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-04-16 19:54:32.630][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-04-16 19:54:32.970][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:32.972][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-04-16 19:54:32.999][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-04-16 19:54:33.004][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-04-16 19:54:33.008][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:33.010][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:33.011][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:33.013][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:33.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:33.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:33.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:33.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:33.023][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:33.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:33.026][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:33.028][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:33.029][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.030][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:33.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:33.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.037][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:33.038][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:33.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.041][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.042][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:33.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:33.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.049][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:33.051][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:33.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.054][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.055][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:33.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:33.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.061][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:33.069][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:33.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.077][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.079][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:33.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:33.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.085][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:33.086][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:33.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.104][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.106][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:33.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:33.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.112][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:33.113][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:33.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.115][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.117][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:33.119][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:33.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.121][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.123][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:33.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:33.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.126][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:33.127][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:33.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.129][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.131][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:33.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:33.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.138][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:33.139][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:33.141][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.142][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.144][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:33.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:33.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.148][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:33.149][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:33.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.151][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.152][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:33.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:33.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.157][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:33.158][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:33.159][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.161][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.162][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:33.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:33.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:33.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:33.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.171][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:33.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:33.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:33.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:33.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:33.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:33.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:33.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:33.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:33.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:33.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:33.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:33.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:33.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:33.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:33.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:33.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:33.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:33.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:33.242][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-04-16 19:54:33.244][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:33.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:33.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:33.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:33.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:33.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:33.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:33.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:33.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:33.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:33.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:33.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:33.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:33.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:33.271][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:33.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:33.273][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-04-16 19:54:33.274][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:33.276][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-04-16 19:54:33.278][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:33.279][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:33.281][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:33.282][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:33.284][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:33.285][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:33.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:33.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:33.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:33.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:33.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:33.299][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:33.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:33.317][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-04-16 19:54:33.322][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:33.324][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:33.326][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-04-16 19:54:33.667][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-04-16 19:54:40.188][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:40.190][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-04-16 19:54:40.195][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-04-16 19:54:40.199][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-04-16 19:54:40.201][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:40.203][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:40.204][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:40.206][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:40.207][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:40.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:40.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:40.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:40.218][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:40.218][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.TRACE[2025-04-16 19:54:40.222][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:40.224][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:40.225][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.226][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:40.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:40.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.232][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:40.233][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:40.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.235][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.250][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:40.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:40.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.257][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:40.258][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:40.259][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.260][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.261][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:40.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:40.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.267][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:40.268][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:40.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.271][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.273][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:40.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:40.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.278][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:40.279][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:40.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.282][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.283][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:40.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:40.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.289][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:40.290][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:40.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.293][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.294][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:40.296][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:40.298][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.299][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.300][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:40.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:40.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.306][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:40.307][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:40.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.310][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.311][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:40.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:40.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.317][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:40.318][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:40.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.321][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.323][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:40.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:40.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.329][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:40.330][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:40.331][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.333][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.335][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:40.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:40.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.341][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:40.343][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:40.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.345][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.360][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:40.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:40.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.374][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:40.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:40.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:40.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:40.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:40.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:40.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:40.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:40.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:40.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:40.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:40.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:40.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:40.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:40.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:40.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:40.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:40.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:40.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:40.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:40.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:40.434][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-04-16 19:54:40.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:40.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:40.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:40.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:40.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:40.446][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:40.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:40.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:40.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:40.451][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:40.452][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:40.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:40.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:40.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:40.461][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:40.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:40.464][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-04-16 19:54:40.465][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:40.467][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-04-16 19:54:40.469][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:40.470][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:40.472][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:40.473][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:40.474][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:40.475][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:40.478][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:40.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:40.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:40.487][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:40.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:40.490][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:40.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:40.493][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-04-16 19:54:40.496][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:40.498][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:40.499][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-04-16 19:54:40.843][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-04-16 19:54:41.186][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:41.188][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-04-16 19:54:41.193][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-04-16 19:54:41.197][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-04-16 19:54:41.199][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:41.201][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:41.202][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:41.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:41.205][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:41.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:41.213][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:41.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:41.222][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:41.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:41.230][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:41.232][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:41.233][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.235][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:41.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:41.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.240][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:41.242][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:41.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.244][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.245][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:41.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:41.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.250][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:41.251][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:41.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.253][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.255][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:41.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:41.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.260][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:41.261][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:41.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.263][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.264][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:41.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:41.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.269][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:41.270][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:41.271][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.272][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.273][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:41.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:41.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.279][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:41.280][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:41.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.282][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.283][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:41.284][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:41.285][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.286][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.287][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:41.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:41.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.291][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:41.292][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:41.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.294][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:41.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:41.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.299][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:41.300][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:41.302][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.303][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.304][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:41.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:41.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.308][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:41.309][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:41.310][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.311][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.313][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:41.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:41.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.318][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:41.319][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:41.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.321][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.323][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:41.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:41.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:41.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:41.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:41.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:41.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:41.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:41.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.352][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:41.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:41.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:41.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:41.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:41.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:41.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:41.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:41.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:41.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:41.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:41.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:41.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:41.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:41.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:41.384][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-04-16 19:54:41.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:41.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:41.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.389][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:41.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:41.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:41.393][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:41.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:41.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:41.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:41.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:41.398][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:41.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:41.405][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:41.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:41.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:41.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:41.409][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-04-16 19:54:41.410][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:41.412][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-04-16 19:54:41.414][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:41.415][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:41.416][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:41.417][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:41.418][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:41.419][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:41.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:41.424][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:41.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:41.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:41.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:41.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:41.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:41.438][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-04-16 19:54:41.443][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:41.445][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:41.447][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-04-16 19:54:41.782][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-04-16 19:54:42.117][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:42.121][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-04-16 19:54:42.127][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-04-16 19:54:42.142][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-04-16 19:54:42.144][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:42.147][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:42.148][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:42.150][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:42.151][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:42.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:42.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:42.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:42.161][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:42.162][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.TRACE[2025-04-16 19:54:42.164][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:42.166][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:42.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.168][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:42.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:42.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.174][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:42.175][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:42.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.177][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.179][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:42.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:42.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.183][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:42.184][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:42.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.186][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.188][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:42.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:42.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.193][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:42.194][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:42.195][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.197][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.198][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:42.199][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:42.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.201][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.203][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:42.204][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:42.205][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.206][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.208][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:42.209][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:42.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.211][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.213][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:42.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:42.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.218][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:42.219][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:42.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.222][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:42.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:42.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.228][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:42.229][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:42.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.232][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.234][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:42.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:42.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.239][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:42.241][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:42.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.243][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.244][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:42.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:42.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.250][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:42.251][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:42.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.253][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.255][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:42.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:42.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:42.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:42.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:42.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:42.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:42.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:42.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:42.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:42.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:42.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:42.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:42.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:42.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:42.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:42.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:42.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:42.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:42.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:42.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:42.310][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-04-16 19:54:42.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:42.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:42.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:42.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:42.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:42.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:42.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:42.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:42.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:42.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:42.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:42.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:42.336][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:42.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:42.339][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:42.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:42.342][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-04-16 19:54:42.343][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:42.345][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-04-16 19:54:42.347][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:42.348][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:42.349][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:42.350][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:42.351][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:42.352][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:42.354][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:42.355][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:42.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:42.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:42.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:42.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:42.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:42.368][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-04-16 19:54:42.371][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:42.372][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:42.373][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-04-16 19:54:42.709][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-04-16 19:54:43.045][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:43.047][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-04-16 19:54:43.051][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-04-16 19:54:43.066][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-04-16 19:54:43.068][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:43.070][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:43.071][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:43.073][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:43.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:43.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:43.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:43.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:43.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:43.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:43.088][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:43.089][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:43.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.092][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:43.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:43.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.098][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:43.099][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:43.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.101][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.103][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:43.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:43.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.108][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:43.109][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:43.110][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.111][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.112][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:43.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:43.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.116][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:43.117][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:43.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.120][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.121][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:43.123][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:43.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.125][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.126][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:43.127][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:43.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.130][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.132][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:43.134][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:43.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.136][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.138][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:43.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:43.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.143][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:43.144][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:43.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.146][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.147][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:43.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:43.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.152][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:43.153][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:43.154][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.155][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.157][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:43.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:43.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.161][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:43.163][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:43.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.165][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.167][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:43.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:43.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.171][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:43.172][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:43.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.173][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:43.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:43.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:43.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:43.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:43.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:43.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:43.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:43.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:43.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:43.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:43.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:43.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:43.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:43.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:43.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:43.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:43.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:43.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:43.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:43.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:43.224][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-04-16 19:54:43.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:43.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:43.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.231][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:43.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:43.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:43.236][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:43.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:43.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:43.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:43.240][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:43.241][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:43.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:43.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:43.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:43.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:43.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:43.253][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-04-16 19:54:43.254][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:43.255][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-04-16 19:54:43.257][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:43.257][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:43.258][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:43.260][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:43.261][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:43.262][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:43.264][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:43.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:43.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:43.272][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:43.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:43.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:43.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:43.277][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-04-16 19:54:43.280][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:43.281][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:43.283][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-04-16 19:54:43.707][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-04-16 19:54:45.079][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:45.081][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-04-16 19:54:45.085][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-04-16 19:54:45.096][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-04-16 19:54:45.099][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:45.100][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:45.102][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:45.103][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:45.104][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:45.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:45.110][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:45.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:45.112][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:45.113][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.TRACE[2025-04-16 19:54:45.115][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:45.116][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:45.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.118][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:45.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:45.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.124][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:45.126][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:45.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.128][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.129][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:45.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:45.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.132][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:45.134][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:45.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.136][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.137][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:45.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:45.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.141][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:45.142][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:45.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.144][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.145][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:45.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:45.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.150][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:45.151][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:45.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.152][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.154][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:45.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:45.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.157][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:45.158][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:45.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.160][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.162][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:45.162][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:45.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.164][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.165][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:45.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:45.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.169][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:45.170][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:45.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.172][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.173][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:45.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:45.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.176][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:45.178][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:45.179][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.180][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.182][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:45.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:45.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.186][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:45.186][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:45.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.188][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.189][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:45.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:45.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.199][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:45.201][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:45.202][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.203][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.204][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:45.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:45.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:45.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:45.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:45.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:45.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:45.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:45.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:45.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:45.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:45.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:45.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:45.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:45.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:45.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:45.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:45.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:45.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:45.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:45.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:45.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:45.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:45.245][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-04-16 19:54:45.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:45.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:45.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.250][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:45.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:45.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:45.253][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:45.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:45.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:45.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:45.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:45.257][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:45.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:45.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:45.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:45.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:45.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:45.270][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-04-16 19:54:45.271][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:45.273][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-04-16 19:54:45.274][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:45.275][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:45.276][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:45.277][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:45.278][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:45.279][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:45.282][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:45.283][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:45.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:45.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:45.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:45.293][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:45.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:45.295][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-04-16 19:54:45.304][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:45.306][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:45.308][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-04-16 19:54:45.641][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-04-16 19:54:45.984][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:45.986][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-04-16 19:54:45.990][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-04-16 19:54:45.993][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-04-16 19:54:45.994][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:45.997][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:45.998][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:46.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:46.002][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:46.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:46.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:46.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:46.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:46.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:46.017][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:46.018][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:46.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.020][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:46.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:46.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.025][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:46.026][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:46.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.028][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.030][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:46.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:46.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.033][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:46.034][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:46.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.037][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.039][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:46.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:46.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.043][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:46.044][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:46.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.046][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.047][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:46.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:46.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.051][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:46.052][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:46.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.054][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.055][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:46.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:46.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.060][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:46.061][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:46.062][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.063][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.064][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:46.066][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:46.067][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.067][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.069][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:46.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:46.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.073][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:46.074][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:46.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.076][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.077][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:46.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:46.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.081][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:46.082][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:46.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.090][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.096][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:46.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:46.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.103][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:46.105][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:46.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.107][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.108][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:46.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:46.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.112][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:46.113][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:46.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.116][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.117][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:46.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:46.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:46.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:46.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.127][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:46.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:46.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:46.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:46.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.136][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:46.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:46.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:46.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:46.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:46.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:46.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:46.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:46.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:46.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:46.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:46.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:46.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:46.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:46.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:46.169][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-04-16 19:54:46.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:46.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:46.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:46.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:46.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:46.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:46.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:46.181][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:46.182][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:46.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:46.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:46.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:46.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:46.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:46.193][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-04-16 19:54:46.194][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:46.195][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-04-16 19:54:46.197][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:46.198][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:46.199][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:46.200][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:46.201][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:46.208][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:46.212][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:46.213][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:46.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:46.222][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:46.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:46.224][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:46.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:46.227][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-04-16 19:54:46.230][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:46.231][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:46.233][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-04-16 19:54:46.568][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-04-16 19:54:46.915][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:46.918][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-04-16 19:54:46.924][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-04-16 19:54:46.928][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-04-16 19:54:46.930][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:46.931][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:46.932][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:46.933][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:46.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:46.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:46.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:46.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:46.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:46.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:46.949][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:46.950][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:46.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.952][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:46.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:46.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.957][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:46.958][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:46.959][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.959][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.961][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:46.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:46.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.965][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:46.966][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:46.967][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.967][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.969][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:46.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:46.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.972][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:46.974][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:46.974][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.975][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.977][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:46.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:46.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.981][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:46.982][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:46.983][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.984][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.985][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:46.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:46.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.989][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:46.990][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:46.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.992][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.994][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:46.995][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:46.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:46.997][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:46.998][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:47.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:47.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.014][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:47.016][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:47.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.018][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.019][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:47.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:47.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.023][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:47.024][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:47.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.026][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.028][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:47.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:47.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.032][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:47.033][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:47.034][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.035][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.036][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:47.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:47.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.040][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:47.040][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:47.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.042][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.043][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:47.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:47.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.047][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:47.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:47.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:47.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:47.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:47.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:47.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:47.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:47.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:47.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:47.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:47.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:47.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:47.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:47.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:47.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:47.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:47.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:47.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:47.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:47.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:47.087][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-04-16 19:54:47.088][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:47.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:47.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:47.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:47.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:47.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:47.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:47.102][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:47.103][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:47.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:47.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:47.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:47.125][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:47.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:47.128][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-04-16 19:54:47.130][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:47.132][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-04-16 19:54:47.134][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:47.136][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:47.138][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:47.139][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:47.141][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:47.142][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:47.147][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:47.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:47.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:47.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:47.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:47.161][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:47.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:47.165][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-04-16 19:54:47.169][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:47.171][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:47.173][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-04-16 19:54:47.514][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-04-16 19:54:47.856][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:47.858][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-04-16 19:54:47.863][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-04-16 19:54:47.867][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-04-16 19:54:47.869][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:47.870][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:47.871][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:47.872][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:47.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:47.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:47.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:47.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:47.882][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:47.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:47.885][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:47.886][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:47.887][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.888][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:47.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:47.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.893][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:47.894][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:47.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.896][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.897][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:47.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:47.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.901][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:47.902][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:47.902][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.903][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.904][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:47.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:47.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.908][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:47.909][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:47.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.911][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.912][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:47.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:47.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.918][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:47.919][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:47.920][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.932][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.934][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:47.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:47.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.939][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:47.941][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:47.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.942][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.944][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:47.945][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:47.947][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.948][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.949][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:47.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:47.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.952][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:47.953][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:47.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.955][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:47.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:47.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.960][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:47.961][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:47.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.962][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:47.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:47.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.968][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:47.970][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:47.971][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.972][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.973][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:47.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:47.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.977][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:47.978][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:47.979][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.979][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.980][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:47.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:47.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:47.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:47.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:47.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:47.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:47.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:47.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:47.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:47.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:47.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:48.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:48.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:48.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:48.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:48.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:48.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:48.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:48.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:48.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:48.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:48.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:48.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:48.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:48.024][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-04-16 19:54:48.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:48.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:48.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:48.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:48.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.041][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:48.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:48.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:48.045][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:48.046][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:48.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:48.054][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:48.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:48.056][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:48.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:48.059][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-04-16 19:54:48.060][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:48.061][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-04-16 19:54:48.063][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:48.064][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:48.065][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:48.066][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:48.067][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:48.067][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:48.070][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:48.071][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:48.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:48.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:48.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:48.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:48.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:48.083][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-04-16 19:54:48.087][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:48.088][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:48.089][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-04-16 19:54:48.438][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-04-16 19:54:48.787][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:48.789][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-04-16 19:54:48.794][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-04-16 19:54:48.796][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-04-16 19:54:48.798][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:48.799][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:48.800][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:48.803][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:48.804][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:48.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:48.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:48.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:48.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:48.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:48.817][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:48.818][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:48.818][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.819][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:48.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:48.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.825][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:48.827][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:48.828][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.829][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.831][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:48.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:48.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.834][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:48.836][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:48.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.838][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.850][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:48.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:48.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.856][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:48.857][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:48.858][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.858][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.859][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:48.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:48.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.863][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:48.864][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:48.865][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.866][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.868][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:48.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:48.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.872][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:48.874][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:48.874][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.875][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.876][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:48.877][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:48.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.880][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.881][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:48.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:48.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.886][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:48.887][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:48.888][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.890][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:48.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:48.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.897][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:48.898][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:48.899][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.900][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.901][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:48.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:48.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.906][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:48.906][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:48.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.909][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.912][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:48.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:48.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.917][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:48.918][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:48.919][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.920][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.922][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:48.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:48.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.926][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:48.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:48.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:48.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:48.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:48.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:48.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:48.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:48.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:48.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:48.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:48.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:48.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:48.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:48.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:48.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:48.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:48.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:48.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:48.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:48.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:48.979][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-04-16 19:54:48.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:48.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:48.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.986][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:48.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:48.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:48.990][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:48.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:48.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:48.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:48.994][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:48.995][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:48.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:49.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:49.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:49.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:49.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:49.006][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-04-16 19:54:49.007][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:49.009][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-04-16 19:54:49.010][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:49.011][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:49.012][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:49.014][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:49.015][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:49.016][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:49.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:49.020][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:49.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:49.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:49.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:49.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:49.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:49.033][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-04-16 19:54:49.035][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:49.036][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:49.038][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-04-16 19:54:49.374][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-04-16 19:54:49.710][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2025-04-16 19:54:49.712][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-04-16 19:54:49.715][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-04-16 19:54:49.720][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-04-16 19:54:49.724][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-04-16 19:54:49.726][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:49.728][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:49.729][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:49.731][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:49.733][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:49.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:49.741][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:49.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:49.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:49.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:49.747][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:49.748][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:49.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.757][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:49.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:49.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.768][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:49.769][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:49.770][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.771][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.773][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:49.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:49.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.777][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:49.779][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:49.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.781][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.782][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:49.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:49.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.786][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:49.787][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:49.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.790][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.792][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:49.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:49.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.796][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:49.797][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:49.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.800][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.801][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:49.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:49.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.807][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:49.808][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:49.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.811][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.812][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:49.813][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:49.814][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.816][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.817][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:49.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:49.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.822][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:49.823][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:49.824][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.825][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:49.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:49.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.832][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:49.834][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:49.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.836][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.838][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:49.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:49.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.844][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:49.846][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:49.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.848][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.850][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:49.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:49.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.855][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:49.857][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:49.858][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.860][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.861][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:49.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:49.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:49.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:49.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:49.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:49.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:49.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:49.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.887][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:49.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:49.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:49.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:49.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:49.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:49.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:49.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:49.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:49.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:49.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:49.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:49.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:49.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:49.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:49.921][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-04-16 19:54:49.923][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:49.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:49.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:49.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:49.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:49.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:49.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:49.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:49.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:49.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:49.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:49.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:49.945][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:49.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:49.947][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:49.948][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[2025-04-16 19:54:49.949][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-04-16 19:54:49.951][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:49.952][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-04-16 19:54:49.954][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:49.955][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:49.956][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:49.957][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:49.958][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:49.960][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:49.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:49.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:49.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:49.972][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:49.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:49.974][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:49.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:49.976][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-04-16 19:54:49.980][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:49.981][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:49.983][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-04-16 19:54:50.901][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-04-16 19:54:51.237][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:51.241][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-04-16 19:54:51.246][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-04-16 19:54:51.250][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-04-16 19:54:51.253][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:51.267][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:51.270][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:51.272][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:51.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:51.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:51.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:51.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:51.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:51.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:51.291][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:51.293][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:51.294][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.296][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:51.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:51.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.302][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:51.303][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:51.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.305][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.307][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:51.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:51.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.312][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:51.313][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:51.315][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.316][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.318][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:51.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:51.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.324][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:51.326][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:51.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.328][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.330][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:51.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:51.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.335][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:51.337][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:51.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.340][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.341][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:51.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:51.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.347][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:51.349][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:51.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.351][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.353][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:51.354][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:51.356][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.357][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.358][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:51.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:51.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.364][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:51.366][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:51.367][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.368][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:51.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:51.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.376][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:51.377][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:51.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.379][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.382][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:51.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:51.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.387][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:51.389][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:51.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.391][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.393][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:51.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:51.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.399][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:51.408][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:51.410][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.411][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.413][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:51.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:51.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:51.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:51.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:51.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:51.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:51.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:51.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:51.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:51.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:51.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:51.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:51.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:51.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:51.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:51.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:51.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:51.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:51.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:51.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:51.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:51.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:51.469][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-04-16 19:54:51.471][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:51.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:51.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:51.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:51.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:51.482][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:51.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:51.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:51.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:51.517][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:54:51.522][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:51.524][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:51.527][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-16 19:54:51.934][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-16 19:54:52.339][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:52.342][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-04-16 19:54:52.356][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-04-16 19:54:52.367][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:52.369][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:52.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:52.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:52.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:52.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:52.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:52.384][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.389][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:52.400][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:52.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:52.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:52.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:52.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:52.414][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:52.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:52.417][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.423][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.429][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.434][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:52.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:52.446][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:52.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:52.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:52.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:52.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:52.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:52.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.480][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.486][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:52.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:52.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:52.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:52.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:52.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:52.677][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:52.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:52.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.686][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.696][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.701][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:52.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:52.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:52.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:52.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:52.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:52.738][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:52.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:52.741][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.752][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:52.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:52.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:52.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:52.773][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:52.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:52.781][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:52.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:52.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.789][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:52.799][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:52.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:52.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:52.809][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:52.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:52.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:52.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:52.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.825][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:52.830][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:52.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:52.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:52.840][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:52.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:52.842][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:52.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:52.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.851][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.857][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:52.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:52.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:52.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:52.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:52.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:52.876][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:52.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:52.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.890][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:52.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:52.897][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:52.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:52.907][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:52.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:52.911][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:52.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:52.914][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.920][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:52.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:52.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:52.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:52.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:52.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:52.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:52.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:52.948][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.959][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:52.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:52.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:52.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:52.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:52.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:52.978][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:52.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:52.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.985][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:52.991][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:52.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:52.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:52.997][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:52.998][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:52.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:53.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:53.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:53.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:53.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:53.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:53.020][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:53.031][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:53.038][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:53.045][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:53.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:53.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:53.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:53.064][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:53.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:53.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:53.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:53.090][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:53.099][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:53.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:53.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:53.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:53.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:53.124][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:53.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:53.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:53.145][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:53.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:53.168][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:53.169][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:53.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:53.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:53.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:53.184][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:53.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:53.204][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:53.213][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:53.233][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:53.261][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:53.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:53.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:53.290][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:53.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:53.293][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:53.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:53.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:53.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:53.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:53.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:53.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:53.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:53.357][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:53.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:53.360][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:53.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:53.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:53.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:53.404][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:53.417][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:53.418][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:53.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:53.448][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:53.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:53.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:53.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:53.470][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:53.480][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:53.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:53.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:53.527][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:53.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:53.541][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:53.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:53.544][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:53.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:53.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:53.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:53.576][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:53.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:53.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:53.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:53.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:53.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:53.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:53.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:53.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:53.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:53.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:53.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:53.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:53.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:53.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:53.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:53.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:53.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:53.775][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.INFO [2025-04-16 19:54:53.780][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2025-04-16 19:54:53.783][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:53.784][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:53.791][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-16 19:54:54.133][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-16 19:54:54.469][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:54.473][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-04-16 19:54:54.479][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-04-16 19:54:54.486][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:54:54.491][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:54.493][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:54.496][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-16 19:54:54.834][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-16 19:54:55.172][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:55.175][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-04-16 19:54:55.181][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-04-16 19:54:55.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:55.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:55.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:55.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:55.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:55.199][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:55.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:55.202][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-04-16 19:54:55.204][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:55.206][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-04-16 19:54:55.207][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:55.209][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:55.210][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:55.212][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:55.213][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:55.214][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:55.218][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:55.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:55.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:55.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:55.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:55.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:55.233][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[2025-04-16 19:54:55.235][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-04-16 19:54:55.239][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:55.240][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:55.242][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-04-16 19:54:55.591][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-04-16 19:54:55.943][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:55.946][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-04-16 19:54:55.952][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-04-16 19:54:55.956][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-04-16 19:54:55.958][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:55.960][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:55.962][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:55.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:55.965][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:55.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:55.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:55.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:55.978][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:55.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:55.983][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:55.984][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:55.985][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:55.987][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:55.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:55.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:55.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:55.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:55.994][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:55.995][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:55.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:55.998][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:55.999][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:56.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:56.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.005][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:56.006][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:56.008][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.009][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.011][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:56.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:56.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.016][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:56.018][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:56.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.020][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.022][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:56.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:56.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.027][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:56.029][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:56.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.031][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.033][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:56.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:56.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.039][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:56.040][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:56.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.043][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.045][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:56.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:56.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.050][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:56.052][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:56.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.054][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.056][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:56.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:56.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.061][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:56.063][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:56.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.065][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:56.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:56.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.073][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:56.074][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:56.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.077][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.079][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:56.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:56.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.084][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:56.086][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:56.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.088][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.090][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:56.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:56.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.096][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:56.097][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:56.099][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.100][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.102][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:56.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:56.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:56.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:56.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:56.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:56.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:56.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:56.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.124][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:56.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:56.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:56.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:56.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:56.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:56.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:56.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:56.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:56.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:56.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:56.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:56.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:56.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:56.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:56.187][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-04-16 19:54:56.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:56.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:56.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:56.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:56.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:56.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:56.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:56.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:56.221][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:56.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:56.247][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:56.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:56.250][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:56.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:56.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:56.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:56.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:56.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:56.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:56.277][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:56.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:56.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:56.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:56.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:56.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:56.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:56.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:56.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:56.346][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:56.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:56.349][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-04-16 19:54:56.350][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:54:56.363][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-04-16 19:54:56.365][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:54:56.367][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:54:56.370][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:54:56.379][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:54:56.381][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:54:56.382][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:54:56.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:56.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:56.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:56.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:56.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:56.409][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:56.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:54:56.412][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-04-16 19:54:56.423][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:56.425][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:56.427][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-04-16 19:54:56.786][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-04-16 19:54:57.136][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:57.139][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-04-16 19:54:57.144][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-04-16 19:54:57.148][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-04-16 19:54:57.152][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:54:57.154][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:54:57.156][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:54:57.158][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:57.159][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:57.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:57.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:57.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:57.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:57.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:57.177][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:57.178][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:57.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.197][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:57.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:57.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.205][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:57.207][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:57.209][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.211][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.214][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:54:57.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:54:57.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.224][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:57.225][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:57.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.228][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.230][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:54:57.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:54:57.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.235][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:57.237][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:57.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.239][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.241][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:54:57.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:54:57.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.246][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:57.248][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:57.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.250][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.252][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:54:57.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:54:57.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.258][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:57.259][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:54:57.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.262][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.263][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:57.265][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:57.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.267][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.269][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:54:57.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:54:57.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.274][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:57.276][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:57.277][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.278][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:57.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:57.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.286][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:57.287][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:57.288][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.290][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.291][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:54:57.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:54:57.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.297][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:57.299][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:57.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.301][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.303][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:54:57.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:54:57.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.309][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:57.310][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:57.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.313][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.314][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:54:57.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:54:57.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:57.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:57.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:57.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:57.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:57.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:57.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:54:57.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:54:57.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:57.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:57.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:57.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:57.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:57.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:57.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:57.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:57.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:57.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:57.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:54:57.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:54:57.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:57.384][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-04-16 19:54:57.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:57.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:57.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.400][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:57.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:57.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:57.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:57.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:57.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:57.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:57.458][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:54:57.478][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:54:57.480][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:54:57.483][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-16 19:54:58.658][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-16 19:54:59.067][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:54:59.070][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-04-16 19:54:59.077][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-04-16 19:54:59.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:59.084][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:59.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:59.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:59.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:59.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:59.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:59.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:59.116][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:59.117][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:59.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:59.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:59.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:59.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:59.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:59.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:59.161][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:59.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:59.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:59.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:59.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:59.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:59.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:59.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.195][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:59.206][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:59.207][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:59.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:59.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:59.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:59.220][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:59.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:59.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.229][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.240][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.246][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:59.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:59.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:59.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:59.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:59.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:59.292][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:59.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:59.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.307][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:59.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:59.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:59.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:59.324][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:59.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:59.328][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:59.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:59.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.349][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:59.377][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:59.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:59.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:59.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:59.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:59.410][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:59.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:59.419][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.426][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:59.451][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:59.453][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:59.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:59.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:59.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:59.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:59.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:59.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:59.529][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:59.530][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:59.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:59.541][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:59.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:59.544][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:59.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:59.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.571][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:59.578][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:59.579][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:59.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:59.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:59.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:59.601][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:59.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:59.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.616][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:59.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:59.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:59.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:59.665][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:59.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:59.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:59.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:59.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.684][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.695][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:59.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:59.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:59.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:59.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:59.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:59.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:59.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:59.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.735][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:59.766][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:59.768][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:59.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:59.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:59.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:59.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:59.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:59.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:59.846][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:59.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:59.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:59.882][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:59.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:59.886][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:59.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:59.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:54:59.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:54:59.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:54:59.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:54:59.951][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:54:59.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:54:59.955][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:54:59.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:54:59.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.973][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:54:59.986][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:54:59.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:54:59.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:00.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:00.002][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:00.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:00.031][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:00.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:00.035][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:00.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:00.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.057][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:00.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:00.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:00.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:00.102][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:00.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:00.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:00.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:00.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:00.156][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:00.166][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:00.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:00.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:00.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:00.182][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:00.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:00.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.210][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:00.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:00.239][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:00.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:00.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:00.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:00.271][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:00.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:00.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:00.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:00.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:00.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:00.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:00.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:00.347][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:00.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:00.357][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.366][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:00.450][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:00.471][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-16 19:55:00.473][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-16 19:55:00.475][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-16 19:55:00.477][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-16 19:55:00.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:00.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:00.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:00.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:00.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:00.527][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:00.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:00.531][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.552][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:00.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:00.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:00.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:00.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:00.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:00.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:00.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:00.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:00.646][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:00.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:00.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:00.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:00.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:00.672][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:00.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:00.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.688][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.707][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:00.732][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:00.733][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:00.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:00.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:00.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:00.746][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:00.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:00.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.762][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:00.808][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:00.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:00.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:00.821][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:00.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:00.824][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:00.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:00.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:00.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:00.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:00.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:00.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:00.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:00.896][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:00.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:00.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:00.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:00.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:00.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:00.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:00.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:00.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:00.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:00.952][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:00.989][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:00.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:00.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:01.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:01.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:01.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:01.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:01.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:01.026][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:01.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:01.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.054][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:01.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:01.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:01.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:01.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:01.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:01.091][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:01.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:01.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.111][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:01.134][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:01.143][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:01.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:01.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:01.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:01.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:01.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:01.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:01.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:01.208][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:01.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:01.221][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:01.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:01.224][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:01.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:01.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:01.263][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:01.264][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:01.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:01.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:01.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:01.288][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:01.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:01.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.307][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:01.332][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:01.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:01.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:01.345][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:01.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:01.348][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:01.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:01.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.365][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:01.396][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:01.397][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:01.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:01.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:01.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:01.424][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:01.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:01.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:01.458][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:01.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:01.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:01.487][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:01.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:01.491][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:01.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:01.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.505][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:01.524][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:01.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:01.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:01.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:01.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:01.546][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:01.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:01.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:01.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:01.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:01.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:01.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:01.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:01.613][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:01.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:01.616][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.628][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.655][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:01.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:01.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:01.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:01.676][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:01.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:01.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:01.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:01.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.691][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:01.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:01.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:01.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:01.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:01.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:01.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:01.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:01.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:01.766][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:01.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:01.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:01.785][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:01.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:01.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:01.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:01.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.803][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:01.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.848][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-16 19:55:01.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-16 19:55:01.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-16 19:55:01.898][biodb::testThat]
biodb.INFO [2025-04-16 19:55:01.899][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-04-16 19:55:01.901][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:55:01.902][biodb::testThat]
biodb.TRACE[2025-04-16 19:55:01.913][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-16 19:55:01.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-16 19:55:01.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.921][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:01.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:01.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:01.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:01.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:01.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:01.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:01.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:01.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:01.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:01.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:01.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:01.965][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:01.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:01.978][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:01.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:01.980][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:01.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:01.989][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:01.993][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:55:01.995][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:55:01.997][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-16 19:55:02.359][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-16 19:55:02.697][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:55:02.700][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-04-16 19:55:02.706][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-04-16 19:55:02.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:02.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:02.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:02.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:02.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:02.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:02.725][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.TRACE[2025-04-16 19:55:02.727][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:02.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:02.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:02.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:02.733][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:02.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:02.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:02.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:02.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:02.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:02.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:02.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:02.745][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:02.749][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:55:02.751][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:55:02.753][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-16 19:55:03.093][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-16 19:55:03.432][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:55:03.435][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-04-16 19:55:03.441][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-04-16 19:55:03.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:03.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:03.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:03.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:03.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:03.460][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:03.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:03.463][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:03.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:03.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.469][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:03.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:03.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:03.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:03.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:03.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:03.482][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:03.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:03.491][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:03.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:03.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:03.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:03.497][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:03.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:03.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.502][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:03.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:03.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.508][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:03.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:03.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:03.513][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-16 19:55:03.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:03.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:03.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:03.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:03.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:03.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:03.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:03.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.542][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:03.543][private$selectFields]
biodb.TRACE[2025-04-16 19:55:03.544][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-16 19:55:03.546][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-16 19:55:03.547][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:03.548][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.550][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.551][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.552][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.553][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.555][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.557][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.559][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:03.560][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:03.561][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.563][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.564][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.565][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.567][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-16 19:55:03.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.614][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-04-16 19:55:03.616][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:03.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:03.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:03.626][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:03.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:03.629][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:03.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:03.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.648][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:03.655][private$selectFields]
biodb.TRACE[2025-04-16 19:55:03.656][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-16 19:55:03.657][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-16 19:55:03.659][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:03.660][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.661][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.662][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.663][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.664][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.666][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.667][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.668][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.669][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:03.670][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:03.672][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.673][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.674][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.675][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.676][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-16 19:55:03.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.696][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.709][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-16 19:55:03.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:03.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:03.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:03.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:03.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:03.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:03.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:03.727][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.742][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.754][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:03.755][private$selectFields]
biodb.TRACE[2025-04-16 19:55:03.757][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-16 19:55:03.758][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-16 19:55:03.759][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:03.761][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.769][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.772][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.774][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.776][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.778][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.788][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:03.790][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:03.791][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.793][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.796][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.804][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-16 19:55:03.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:03.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.839][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-04-16 19:55:03.841][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-16 19:55:03.843][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-16 19:55:03.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:03.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:03.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:03.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:03.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.902][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:03.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:03.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:03.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:03.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:03.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:03.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:04.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:04.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:04.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:04.102][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:04.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:04.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:04.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:04.119][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:04.125][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:55:04.134][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:55:04.138][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-16 19:55:04.616][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-16 19:55:04.959][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:55:04.963][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-04-16 19:55:04.970][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-04-16 19:55:04.978][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:04.984][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:55:04.986][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:55:04.989][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-16 19:55:05.330][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-16 19:55:05.674][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:55:05.680][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-04-16 19:55:05.691][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-04-16 19:55:05.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:05.701][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:05.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:05.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:05.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:05.722][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:05.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:05.727][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:05.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:05.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:05.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:05.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:05.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:05.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:05.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:05.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:05.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:05.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:05.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:05.750][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:05.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:05.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:05.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:05.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:05.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:05.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:05.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:05.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:05.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:05.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:05.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:05.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:05.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:05.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:05.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:05.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:05.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:05.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:05.792][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:05.793][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:05.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:05.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:05.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:05.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:05.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:05.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:05.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:05.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:05.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:05.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:05.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:05.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:05.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:05.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:05.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:05.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:05.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:05.864][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-16 19:55:05.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:05.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:05.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:05.976][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:05.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:05.979][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:05.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:05.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:05.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:05.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:05.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:05.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:05.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:05.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:05.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.008][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:06.010][private$selectFields]
biodb.TRACE[2025-04-16 19:55:06.011][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-16 19:55:06.012][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-16 19:55:06.014][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:06.015][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.017][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.027][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.029][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.031][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.034][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.042][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:06.043][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:06.045][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.047][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.049][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.051][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-16 19:55:06.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.081][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.094][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-04-16 19:55:06.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:06.097][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:06.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:06.106][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:06.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:06.108][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:06.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:06.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.171][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.265][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:06.267][private$selectFields]
biodb.TRACE[2025-04-16 19:55:06.282][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-16 19:55:06.283][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-16 19:55:06.285][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:06.286][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.288][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.297][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.299][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.300][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.302][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.303][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.305][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:06.337][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:06.339][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.340][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.355][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.357][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-16 19:55:06.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.406][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-16 19:55:06.417][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:06.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:06.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:06.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:06.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:06.438][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:06.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:06.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.469][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:06.471][private$selectFields]
biodb.TRACE[2025-04-16 19:55:06.473][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-16 19:55:06.474][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-16 19:55:06.476][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:06.493][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.496][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.499][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.501][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.503][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.526][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.530][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.531][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:06.533][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:06.540][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.543][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.547][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.549][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-16 19:55:06.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:06.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.591][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-04-16 19:55:06.592][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-16 19:55:06.594][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-16 19:55:06.618][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-16 19:55:06.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-16 19:55:06.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-16 19:55:06.645][biodb::testThat]
biodb.INFO [2025-04-16 19:55:06.647][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-04-16 19:55:06.649][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:55:06.650][biodb::testThat]
biodb.TRACE[2025-04-16 19:55:06.659][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-16 19:55:06.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-16 19:55:06.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:06.712][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:06.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:06.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:06.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:06.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:06.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:06.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:06.750][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:06.754][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-16 19:55:06.756][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-04-16 19:55:06.758][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-16 19:55:06.768][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-04-16 19:55:06.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:06.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:06.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:06.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:06.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:06.791][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:06.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:06.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.809][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:06.828][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:06.838][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-16 19:55:06.840][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-04-16 19:55:06.842][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-16 19:55:06.851][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-04-16 19:55:06.855][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:06.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:06.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:06.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:06.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:06.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:06.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:06.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.933][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:06.939][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:06.940][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:06.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:06.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:06.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:06.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:06.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:06.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.978][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:06.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:06.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:06.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:07.000][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-16 19:55:07.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:07.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:07.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:07.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:07.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:07.036][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:07.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:07.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.054][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.066][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:07.067][private$selectFields]
biodb.TRACE[2025-04-16 19:55:07.069][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-16 19:55:07.070][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-16 19:55:07.071][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:07.072][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.074][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.085][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.086][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.088][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.089][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.091][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.101][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:07.103][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:07.104][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.106][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.109][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.110][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-16 19:55:07.125][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.156][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-04-16 19:55:07.158][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:07.159][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:07.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:07.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:07.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:07.171][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:07.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:07.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.204][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:07.206][private$selectFields]
biodb.TRACE[2025-04-16 19:55:07.207][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-16 19:55:07.209][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-16 19:55:07.210][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:07.212][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.221][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.224][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.226][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.228][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.229][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.236][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.238][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:07.240][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:07.242][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.243][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.253][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.255][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-16 19:55:07.257][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.290][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-16 19:55:07.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:07.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:07.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:07.312][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:07.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:07.315][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:07.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:07.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.342][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:07.344][private$selectFields]
biodb.TRACE[2025-04-16 19:55:07.345][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-16 19:55:07.346][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-16 19:55:07.348][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:07.359][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.361][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.363][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.366][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.368][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.376][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.379][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.381][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:07.382][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:07.384][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.386][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.394][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.396][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-16 19:55:07.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.416][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.431][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-04-16 19:55:07.432][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-16 19:55:07.438][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-16 19:55:07.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:07.503][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:07.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:07.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:07.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:07.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:07.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:07.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:07.539][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:07.544][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-16 19:55:07.547][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-04-16 19:55:07.555][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-16 19:55:07.558][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-04-16 19:55:07.563][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:07.573][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-16 19:55:07.575][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-04-16 19:55:07.577][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-16 19:55:07.585][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-04-16 19:55:07.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:07.591][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:07.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:07.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:07.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:07.629][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:07.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:07.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:07.669][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:07.670][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:07.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:07.680][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:07.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:07.684][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:07.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:07.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:07.728][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:07.730][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:07.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:07.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:07.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:07.758][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:07.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:07.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:07.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:07.790][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-16 19:55:07.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:07.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:07.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:07.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:07.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:07.815][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:07.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:07.818][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.848][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:07.849][private$selectFields]
biodb.TRACE[2025-04-16 19:55:07.851][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-16 19:55:07.852][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-16 19:55:07.859][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:07.861][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.863][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.865][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.866][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.868][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.876][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.879][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.881][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:07.883][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:07.884][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.892][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.894][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.896][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.898][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-16 19:55:07.900][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.928][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:07.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:07.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:07.957][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-04-16 19:55:07.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:07.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:07.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:07.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:07.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:07.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:07.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:08.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.010][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.025][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:08.026][private$selectFields]
biodb.TRACE[2025-04-16 19:55:08.034][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-16 19:55:08.036][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-16 19:55:08.038][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:08.039][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.041][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.051][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.053][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.055][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.058][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.066][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:08.068][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:08.070][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.071][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.079][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.081][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-16 19:55:08.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.094][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.101][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.114][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-16 19:55:08.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:08.117][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:08.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:08.144][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:08.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:08.147][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:08.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:08.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.165][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.175][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:08.177][private$selectFields]
biodb.TRACE[2025-04-16 19:55:08.178][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-16 19:55:08.184][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-16 19:55:08.186][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:08.188][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.189][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.191][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.192][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.202][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.204][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.206][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.207][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.209][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:08.210][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:08.216][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.218][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.221][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.222][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-16 19:55:08.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.249][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.261][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-04-16 19:55:08.263][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-16 19:55:08.265][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-16 19:55:08.293][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-16 19:55:08.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-16 19:55:08.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-16 19:55:08.322][biodb::testThat]
biodb.INFO [2025-04-16 19:55:08.324][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-04-16 19:55:08.326][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:55:08.328][biodb::testThat]
biodb.TRACE[2025-04-16 19:55:08.343][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-16 19:55:08.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-16 19:55:08.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.361][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.404][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:08.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:08.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:08.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:08.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:08.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:08.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:08.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:08.468][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:08.473][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-16 19:55:08.476][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-04-16 19:55:08.479][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-16 19:55:08.481][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-04-16 19:55:08.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:08.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:08.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:08.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:08.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:08.522][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:08.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:08.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:08.571][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:08.581][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-16 19:55:08.584][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-04-16 19:55:08.586][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-16 19:55:08.600][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-04-16 19:55:08.605][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:08.607][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:08.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:08.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:08.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:08.642][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:08.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:08.651][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.675][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:08.685][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:08.686][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:08.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:08.702][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:08.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:08.706][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:08.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:08.715][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:08.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:08.753][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-16 19:55:08.762][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:08.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:08.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:08.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:08.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:08.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:08.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:08.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.832][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:08.835][private$selectFields]
biodb.TRACE[2025-04-16 19:55:08.837][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-16 19:55:08.839][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-16 19:55:08.841][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:08.850][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.853][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.857][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.866][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.868][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.870][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.872][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.873][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:08.882][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:08.884][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.886][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.888][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.890][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.898][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-16 19:55:08.900][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.929][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.946][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-04-16 19:55:08.948][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:08.950][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:08.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:08.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:08.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:08.966][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:08.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:08.978][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:08.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:08.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:08.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.009][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:09.011][private$selectFields]
biodb.TRACE[2025-04-16 19:55:09.014][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-16 19:55:09.016][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-16 19:55:09.018][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:09.027][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.029][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.033][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.042][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.045][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.049][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.051][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:09.065][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:09.067][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.070][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.081][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.083][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-16 19:55:09.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.160][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-16 19:55:09.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:09.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:09.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:09.193][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:09.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:09.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:09.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:09.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.231][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:09.240][private$selectFields]
biodb.TRACE[2025-04-16 19:55:09.242][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-16 19:55:09.244][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-16 19:55:09.246][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:09.248][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.256][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.259][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.261][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.263][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.272][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.277][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.279][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:09.287][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:09.290][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.292][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.294][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.302][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.305][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-16 19:55:09.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.359][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-04-16 19:55:09.361][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-16 19:55:09.364][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-16 19:55:09.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:09.507][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:09.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:09.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:09.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:09.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:09.574][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:09.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:09.580][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:09.584][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-16 19:55:09.586][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-04-16 19:55:09.588][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-16 19:55:09.590][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-04-16 19:55:09.594][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:09.599][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-16 19:55:09.601][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-04-16 19:55:09.602][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-16 19:55:09.605][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-04-16 19:55:09.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:09.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:09.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:09.618][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:09.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:09.621][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:09.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:09.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.649][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:09.656][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:09.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:09.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:09.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:09.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:09.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:09.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:09.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:09.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:09.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:09.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:09.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:09.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:09.720][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:09.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:09.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:09.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:09.755][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-16 19:55:09.761][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:09.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:09.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:09.783][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:09.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:09.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:09.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:09.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.800][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.813][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:09.815][private$selectFields]
biodb.TRACE[2025-04-16 19:55:09.817][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-16 19:55:09.818][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-16 19:55:09.820][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:09.826][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.827][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.829][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.831][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.832][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.834][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.845][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.847][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:09.848][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:09.850][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.851][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.858][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.860][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-16 19:55:09.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.891][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-04-16 19:55:09.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:09.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:09.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:09.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:09.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:09.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:09.922][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.TRACE[2025-04-16 19:55:09.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.954][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:09.956][private$selectFields]
biodb.TRACE[2025-04-16 19:55:09.957][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-16 19:55:09.959][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-16 19:55:09.966][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:09.968][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.970][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.971][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.972][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.974][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.980][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.983][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:09.984][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:09.986][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:09.987][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:09.990][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:09.998][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:10.002][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:10.004][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-16 19:55:10.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:10.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:10.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:10.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:10.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:10.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:10.035][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-16 19:55:10.037][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:10.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:10.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:10.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:10.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:10.053][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:10.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:10.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:10.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:10.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:10.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:10.082][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:10.083][private$selectFields]
biodb.TRACE[2025-04-16 19:55:10.085][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-16 19:55:10.086][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-16 19:55:10.088][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:10.089][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.097][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:10.102][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:10.103][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.105][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:10.107][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:10.114][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:10.115][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-16 19:55:10.117][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.119][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:10.122][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:10.130][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-16 19:55:10.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:10.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:10.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:10.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:10.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:10.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:10.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:10.162][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-04-16 19:55:10.165][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-16 19:55:10.166][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-16 19:55:10.213][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-16 19:55:10.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-16 19:55:10.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:10.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-16 19:55:10.246][biodb::testThat]
biodb.INFO [2025-04-16 19:55:10.247][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-04-16 19:55:10.249][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:55:10.250][biodb::testThat]
biodb.DEBUG[2025-04-16 19:55:10.253][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-04-16 19:55:10.260][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:55:10.263][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-04-16 19:55:10.265][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:55:10.266][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:55:10.268][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:55:10.277][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:55:10.280][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:55:10.281][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:55:10.286][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:10.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:10.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:10.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:10.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:10.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:10.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:10.313][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-04-16 19:55:10.347][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:55:10.349][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:55:10.351][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-04-16 19:55:10.702][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-04-16 19:55:11.046][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:55:11.050][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-04-16 19:55:11.056][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-04-16 19:55:11.061][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-04-16 19:55:11.068][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:55:11.070][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:55:11.072][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:55:11.075][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:11.076][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:11.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:11.108][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:11.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:11.112][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:11.113][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.TRACE[2025-04-16 19:55:11.124][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:11.128][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:11.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:11.131][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:11.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:11.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:11.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:11.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:11.144][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:55:11.145][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:55:11.147][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:11.148][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:11.156][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:55:11.158][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:55:11.159][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:11.161][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:11.163][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:55:11.164][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:55:11.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:11.167][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:11.168][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:55:11.170][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:55:11.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:11.172][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:11.174][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:55:11.176][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:55:11.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:11.178][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:11.180][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:55:11.181][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:11.183][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:11.184][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:11.186][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:11.187][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:11.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:11.189][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:11.191][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:55:11.193][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:55:11.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:11.195][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:11.197][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:55:11.199][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:55:11.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:11.201][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:11.203][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:55:11.204][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:55:11.206][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:11.207][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:11.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:11.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:11.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:11.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:11.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:11.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:11.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:11.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:11.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:11.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:11.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:11.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:11.225][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:11.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:11.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:11.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:11.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:11.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:11.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:11.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:11.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:11.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:11.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:11.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:11.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:11.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:11.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:11.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:11.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:11.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:11.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:11.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:11.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:11.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:11.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:11.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:11.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:11.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:11.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:11.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:11.263][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-04-16 19:55:11.265][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-04-16 19:55:11.280][biodb::testThat]
biodb.INFO [2025-04-16 19:55:11.282][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-04-16 19:55:11.283][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:55:11.285][biodb::testThat]
biodb.DEBUG[2025-04-16 19:55:11.299][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-04-16 19:55:11.301][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-04-16 19:55:11.302][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-04-16 19:55:11.305][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-04-16 19:55:11.307][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-04-16 19:55:11.308][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:55:11.310][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:55:11.312][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:55:11.313][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:55:11.324][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:55:11.331][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:11.333][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:11.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:11.352][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:11.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:11.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:11.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:11.358][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-04-16 19:55:11.371][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:55:11.373][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:55:11.375][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-04-16 19:55:11.719][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-04-16 19:55:12.059][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:55:12.062][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-04-16 19:55:12.069][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-04-16 19:55:12.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:12.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:12.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:12.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:12.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:12.089][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:12.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:12.093][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-04-16 19:55:12.097][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:55:12.099][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:55:12.101][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-04-16 19:55:12.453][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-04-16 19:55:12.797][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:55:12.801][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-04-16 19:55:12.806][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-04-16 19:55:12.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:12.809][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:12.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:12.815][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:12.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:12.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:12.818][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[2025-04-16 19:55:12.819][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-04-16 19:55:12.822][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:55:12.823][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:55:12.824][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-04-16 19:55:13.166][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-04-16 19:55:13.512][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:55:13.515][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-04-16 19:55:13.520][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-04-16 19:55:13.523][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-04-16 19:55:13.526][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:55:13.528][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-04-16 19:55:13.529][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-04-16 19:55:13.532][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:13.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:13.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:13.542][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:13.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:13.544][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:13.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:13.547][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:13.549][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:13.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.552][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:13.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:13.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.558][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:55:13.559][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:55:13.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.561][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.562][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:55:13.563][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:55:13.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.566][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.568][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:55:13.569][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:55:13.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.572][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.574][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:55:13.575][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:55:13.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.577][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.579][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:55:13.580][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:55:13.581][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.582][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.584][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:55:13.586][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:13.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.588][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.590][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:13.591][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:13.592][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.593][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.594][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:55:13.596][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:55:13.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.598][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.600][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:55:13.601][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:55:13.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.604][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.605][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:55:13.607][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:55:13.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.609][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:13.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:13.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:13.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:13.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:13.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:13.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.652][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:13.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:13.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:13.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:13.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:13.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:13.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:13.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:13.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:13.669][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:13.670][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:13.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:13.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:13.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:13.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:13.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:13.685][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:13.686][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:13.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.689][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:13.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:13.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.695][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:55:13.696][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:55:13.697][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.698][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.700][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:55:13.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:55:13.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.705][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:55:13.706][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:55:13.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.708][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.710][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:55:13.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:55:13.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.716][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:55:13.718][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:55:13.719][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.720][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.722][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:55:13.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:55:13.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.727][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:55:13.729][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:55:13.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.731][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.733][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:55:13.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:55:13.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.738][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:55:13.740][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:55:13.741][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.743][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.744][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:55:13.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:55:13.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.750][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:55:13.751][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:13.753][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.754][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.756][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:55:13.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:13.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.762][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:13.763][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:13.764][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.766][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:13.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:13.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.773][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:55:13.774][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:55:13.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.776][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.778][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:55:13.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:55:13.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.783][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:55:13.785][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:55:13.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.788][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.791][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:55:13.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:55:13.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.799][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:55:13.801][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:55:13.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.805][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.808][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:55:13.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:55:13.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:13.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:13.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:13.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:13.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:13.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:13.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:13.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:13.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:13.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:13.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:13.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:13.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:13.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:13.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:13.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:13.850][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:13.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:13.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:13.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:13.862][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:13.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:13.866][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:13.867][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:13.868][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.870][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:13.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:13.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.875][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:55:13.876][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:55:13.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.879][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.880][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:55:13.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:55:13.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.885][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:55:13.886][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:55:13.887][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.888][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.889][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:55:13.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:55:13.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.895][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:55:13.896][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:55:13.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.897][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.898][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:55:13.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:55:13.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.903][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:55:13.904][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:55:13.905][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.906][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.907][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:55:13.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:55:13.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.911][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:55:13.913][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:55:13.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.915][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.916][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:55:13.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:55:13.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.922][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:55:13.923][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:13.924][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.924][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.926][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:55:13.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:13.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.931][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:13.932][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:13.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.934][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:13.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:13.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.940][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:55:13.941][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:55:13.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.943][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.944][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:55:13.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:55:13.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.950][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:55:13.951][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:55:13.952][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.953][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.955][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:55:13.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:55:13.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.960][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:55:13.962][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:55:13.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.964][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.965][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:55:13.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:55:13.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:13.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:13.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.975][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:13.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:13.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:13.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:13.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:13.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:13.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:13.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:13.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:13.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:13.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:13.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:13.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:14.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:14.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:14.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:14.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:14.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:14.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:14.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:14.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:14.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:14.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:14.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:14.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:14.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:14.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:14.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:14.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:14.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:14.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:14.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:14.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:14.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:14.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:14.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:14.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:14.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:14.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:14.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:14.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:14.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:14.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:14.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:14.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:14.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:14.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:14.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:14.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:14.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:14.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:14.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:14.053][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-04-16 19:55:14.054][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-04-16 19:55:14.055][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-04-16 19:55:14.077][biodb::testThat]
biodb.INFO [2025-04-16 19:55:14.079][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-04-16 19:55:14.080][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:55:14.081][biodb::testThat]
biodb.INFO [2025-04-16 19:55:14.124][biodb::testThat]
biodb.INFO [2025-04-16 19:55:14.126][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-04-16 19:55:14.127][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:55:14.129][biodb::testThat]
biodb.INFO [2025-04-16 19:55:14.142][biodb::testThat]
biodb.INFO [2025-04-16 19:55:14.143][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-04-16 19:55:14.145][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:55:14.146][biodb::testThat]
biodb.DEBUG[2025-04-16 19:55:14.149][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:14.154][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:55:14.155][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:55:14.158][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-04-16 19:55:14.583][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-04-16 19:55:15.041][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:55:15.044][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-04-16 19:55:15.049][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-04-16 19:55:15.065][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:55:15.066][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:55:15.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:15.069][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:15.071][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:15.072][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:15.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:15.075][ef$get] fields variable is a list.
biodb.INFO [2025-04-16 19:55:15.076][biodb::testThat]
biodb.INFO [2025-04-16 19:55:15.077][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2025-04-16 19:55:15.079][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:55:15.080][biodb::testThat]
biodb.ERROR[2025-04-16 19:55:15.098][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-04-16 19:55:15.120][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-04-16 19:55:15.138][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-16 19:55:15.140][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-16 19:55:15.142][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-16 19:55:15.143][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-16 19:55:15.144][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:15.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:15.147][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:15.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:15.149][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.150][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 [2025-04-16 19:55:15.165][biodb::testContext]
biodb.INFO [2025-04-16 19:55:15.167][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-16 19:55:15.168][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-04-16 19:55:15.170][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-16 19:55:15.171][biodb::testContext]
biodb.INFO [2025-04-16 19:55:15.174][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-16 19:55:15.176][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-16 19:55:15.181][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-16 19:55:15.183][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-16 19:55:15.184][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-16 19:55:15.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.189][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-16 19:55:15.190][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-16 19:55:15.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.193][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[2025-04-16 19:55:15.194][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-16 19:55:15.195][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-16 19:55:15.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.199][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-16 19:55:15.200][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-16 19:55:15.201][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-16 19:55:15.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.205][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[2025-04-16 19:55:15.206][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-16 19:55:15.207][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-16 19:55:15.208][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-16 19:55:15.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.212][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-16 19:55:15.213][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-16 19:55:15.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.218][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-16 19:55:15.219][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-16 19:55:15.220][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-16 19:55:15.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.225][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-16 19:55:15.226][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-16 19:55:15.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.230][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-16 19:55:15.231][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-16 19:55:15.232][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-16 19:55:15.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.236][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-16 19:55:15.237][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-16 19:55:15.238][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-16 19:55:15.239][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-16 19:55:15.241][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-16 19:55:15.242][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-16 19:55:15.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.246][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-16 19:55:15.247][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-16 19:55:15.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.251][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-16 19:55:15.252][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-16 19:55:15.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.257][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-16 19:55:15.258][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-16 19:55:15.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.262][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-16 19:55:15.264][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-16 19:55:15.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.268][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-16 19:55:15.269][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-16 19:55:15.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.273][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-16 19:55:15.275][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-16 19:55:15.376][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-16 19:55:15.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.383][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-16 19:55:15.385][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-16 19:55:15.390][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-16 19:55:15.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.395][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-16 19:55:15.398][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:15.400][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-16 19:55:15.401][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:15.403][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-16 19:55:15.405][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:15.407][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-16 19:55:15.409][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:15.413][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-16 19:55:15.415][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-16 19:55:15.416][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-16 19:55:15.418][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:15.419][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-16 19:55:15.420][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-16 19:55:15.422][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:15.433][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:15.435][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-16 19:55:15.435][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-16 19:55:15.435][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-16 19:55:15.435][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-16 19:55:15.435][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-16 19:55:15.436][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-16 19:55:15.439][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:15.439][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:15.440][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-16 19:55:15.445][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:15.469][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:15.476][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-16 19:55:15.477][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:15.479][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-16 19:55:15.480][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-16 19:55:15.487][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:15.488][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:15.490][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-16 19:55:15.494][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:15.496][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-16 19:55:15.498][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:15.499][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-16 19:55:15.501][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:15.502][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-16 19:55:15.504][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:15.505][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-16 19:55:15.506][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-16 19:55:15.508][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-16 19:55:15.510][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:15.511][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-16 19:55:15.513][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-16 19:55:15.514][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:15.516][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:15.517][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-16 19:55:15.517][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-16 19:55:15.517][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-16 19:55:15.517][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-16 19:55:15.517][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-16 19:55:15.518][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-16 19:55:15.522][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:15.530][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:15.536][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-16 19:55:15.537][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:15.538][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:15.539][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-16 19:55:15.540][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:15.541][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-16 19:55:15.542][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-16 19:55:15.543][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:15.544][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:15.546][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-16 19:55:15.548][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:15.550][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-16 19:55:15.556][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:15.558][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-16 19:55:15.560][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:15.561][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-16 19:55:15.563][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:15.565][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-16 19:55:15.576][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-16 19:55:15.578][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-16 19:55:15.580][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:15.581][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-16 19:55:15.583][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-16 19:55:15.584][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:15.591][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:15.593][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:15.595][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-16 19:55:15.596][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:15.598][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:15.599][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-16 19:55:15.601][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:15.609][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:15.611][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-16 19:55:15.613][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:15.614][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-16 19:55:15.616][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-16 19:55:15.618][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:15.626][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:15.628][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-16 19:55:15.630][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:15.632][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-16 19:55:15.634][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:15.640][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-16 19:55:15.642][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:15.644][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-16 19:55:15.645][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:15.647][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-16 19:55:15.648][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-16 19:55:15.656][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-16 19:55:15.658][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:15.678][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-16 19:55:15.680][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-16 19:55:15.681][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:15.683][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:15.684][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:15.686][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-16 19:55:15.691][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:15.693][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:15.694][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-16 19:55:15.696][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:15.721][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:15.723][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-16 19:55:15.724][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:15.726][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-16 19:55:15.727][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-16 19:55:15.728][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:15.737][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:15.739][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-16 19:55:15.741][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:15.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:15.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:15.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:15.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:15.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:15.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:15.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:15.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.807][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[2025-04-16 19:55:15.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:15.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:15.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.814][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[2025-04-16 19:55:15.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:15.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:15.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:15.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:15.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.841][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[2025-04-16 19:55:15.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:15.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:15.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:15.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:15.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:15.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:15.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.874][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[2025-04-16 19:55:15.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:15.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:15.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.887][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[2025-04-16 19:55:15.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:15.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:15.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:15.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:15.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:15.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:15.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:15.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:15.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.931][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[2025-04-16 19:55:15.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:15.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:15.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:15.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:15.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:15.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:15.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:15.967][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-16 19:55:15.969][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-16 19:55:15.971][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-16 19:55:15.981][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-16 19:55:15.984][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-16 19:55:15.986][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-16 19:55:15.988][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-16 19:55:15.990][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-16 19:55:16.002][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-16 19:55:16.004][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-16 19:55:16.006][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-16 19:55:16.008][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-16 19:55:16.020][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-16 19:55:16.023][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-16 19:55:16.025][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-16 19:55:16.027][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-16 19:55:16.036][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-16 19:55:16.038][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-16 19:55:16.040][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-16 19:55:16.043][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-16 19:55:16.052][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-16 19:55:16.054][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-16 19:55:16.057][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-16 19:55:16.059][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-16 19:55:16.061][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-16 19:55:16.069][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-16 19:55:16.071][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-16 19:55:16.073][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-16 19:55:16.075][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-16 19:55:16.085][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-16 19:55:16.087][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-16 19:55:16.090][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-16 19:55:16.092][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-16 19:55:16.099][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-16 19:55:16.101][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-16 19:55:16.103][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-16 19:55:16.105][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-16 19:55:16.107][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-16 19:55:16.116][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-16 19:55:16.119][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-16 19:55:16.121][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-16 19:55:16.123][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-16 19:55:16.132][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-16 19:55:16.134][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-16 19:55:16.137][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-16 19:55:16.139][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-16 19:55:16.148][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-16 19:55:16.151][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-16 19:55:16.154][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-16 19:55:16.156][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-16 19:55:16.166][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-16 19:55:16.168][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-16 19:55:16.170][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-16 19:55:16.172][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-16 19:55:16.180][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-16 19:55:16.183][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-16 19:55:16.185][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-16 19:55:16.187][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-16 19:55:16.190][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-16 19:55:16.197][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-16 19:55:16.200][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-16 19:55:16.202][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-16 19:55:16.205][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-16 19:55:16.213][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-16 19:55:16.215][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-16 19:55:16.218][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-16 19:55:16.220][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-16 19:55:16.227][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-16 19:55:16.230][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-16 19:55:16.233][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-16 19:55:16.235][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-16 19:55:16.245][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-16 19:55:16.248][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-16 19:55:16.251][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-16 19:55:16.253][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-16 19:55:16.255][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-16 19:55:16.257][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-16 19:55:16.260][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-16 19:55:16.262][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-16 19:55:16.264][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-16 19:55:16.270][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-16 19:55:16.273][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-16 19:55:16.275][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-16 19:55:16.277][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-16 19:55:16.287][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-16 19:55:16.289][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-16 19:55:16.291][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:16.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:16.293][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:16.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:16.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:16.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:16.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:16.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:16.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:16.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:16.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:16.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:16.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:16.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:16.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:16.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:16.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:16.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:16.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:16.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:16.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:16.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:16.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:16.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:16.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:16.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:16.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:16.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:16.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:16.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:16.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:16.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:16.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:16.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:16.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:16.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:16.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:16.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:16.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:16.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:16.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:16.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:16.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:16.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:16.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:16.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:16.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:16.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:16.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:16.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:16.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:16.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:16.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:16.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:16.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:16.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:16.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:16.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:16.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:16.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:16.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:16.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:16.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:16.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:16.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:16.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:16.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:16.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:16.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:16.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:16.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:16.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:16.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:16.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:16.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:16.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:16.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:16.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:16.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:16.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:16.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:16.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:16.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:16.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:16.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:16.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:16.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:16.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:16.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:16.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:16.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:16.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:16.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:16.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:16.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:16.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:16.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:16.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:16.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:16.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:16.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:16.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:16.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:16.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:16.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:16.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:16.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:16.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:16.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:16.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:16.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:16.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:16.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:16.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:16.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:16.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:16.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:16.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:16.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:16.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:16.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:16.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:16.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:16.635][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-16 19:55:16.638][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-16 19:55:16.641][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:16.643][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-16 19:55:16.650][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:16.652][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-16 19:55:16.653][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:16.655][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-16 19:55:16.657][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:16.665][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-16 19:55:16.667][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-16 19:55:16.669][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-16 19:55:16.671][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:16.673][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-16 19:55:16.681][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-16 19:55:16.683][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-16 19:55:16.683][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-16 19:55:16.683][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-16 19:55:16.683][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-16 19:55:16.683][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-16 19:55:16.683][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-16 19:55:16.683][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-16 19:55:16.683][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-16 19:55:16.683][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-16 19:55:16.683][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-16 19:55:16.683][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-16 19:55:16.685][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:16.722][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-16 19:55:16.722][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-16 19:55:16.722][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-16 19:55:16.726][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-16 19:55:16.735][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:16.737][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:16.739][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-16 19:55:16.741][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:16.743][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:16.744][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-16 19:55:16.746][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:55:16.746][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-16 19:55:16.748][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-16 19:55:16.749][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-16 19:55:16.757][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:16.759][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-16 19:55:16.759][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-16 19:55:16.761][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-16 19:55:16.764][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-16 19:55:16.774][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-16 19:55:16.777][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-16 19:55:16.780][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-16 19:55:16.789][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-16 19:55:16.796][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-16 19:55:16.806][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-16 19:55:16.809][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-16 19:55:16.812][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-16 19:55:16.815][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-16 19:55:16.823][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-16 19:55:16.826][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-16 19:55:16.828][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-16 19:55:16.831][biodb::testThat]
biodb.INFO [2025-04-16 19:55:16.838][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2025-04-16 19:55:16.840][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:55:16.841][biodb::testThat]
biodb.DEBUG[2025-04-16 19:55:16.855][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-16 19:55:16.861][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:55:16.871][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:55:16.873][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-04-16 19:55:17.222][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-04-16 19:55:17.717][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:55:17.721][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-04-16 19:55:17.726][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-04-16 19:55:17.732][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:17.737][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:55:17.738][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:55:17.741][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-16 19:55:18.082][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-16 19:55:18.419][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:55:18.422][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-04-16 19:55:18.428][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-04-16 19:55:18.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:18.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:18.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:18.442][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:18.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:18.445][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:18.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:18.449][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:18.454][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:55:18.456][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:55:18.458][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-16 19:55:18.799][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-16 19:55:19.151][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:55:19.155][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-04-16 19:55:19.162][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-04-16 19:55:19.167][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:19.169][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:19.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:19.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:19.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:19.184][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:19.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:19.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:19.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:19.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:19.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:19.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:19.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:19.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:19.243][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:19.248][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-16 19:55:19.251][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-04-16 19:55:19.253][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-16 19:55:19.255][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-04-16 19:55:19.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:19.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:19.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:19.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:19.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:19.275][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:19.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:19.279][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:19.284][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-16 19:55:19.286][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-04-16 19:55:19.289][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-16 19:55:19.291][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-04-16 19:55:19.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:19.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:19.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:19.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:19.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:19.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:19.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:19.311][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:19.312][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:19.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:19.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:19.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:19.324][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:19.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:19.331][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:19.336][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-16 19:55:19.338][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-04-16 19:55:19.340][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-16 19:55:19.342][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-04-16 19:55:19.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:19.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:19.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:19.356][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:19.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:19.359][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:19.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:19.362][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:19.367][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-16 19:55:19.369][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-04-16 19:55:19.370][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-16 19:55:19.372][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-04-16 19:55:19.375][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:19.376][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:19.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:19.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:19.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:19.384][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:19.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:19.388][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:19.392][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:55:19.392][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:55:19.394][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-16 19:55:19.732][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-16 19:55:20.085][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:55:20.088][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-04-16 19:55:20.091][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-04-16 19:55:20.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:20.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:20.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:20.100][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:20.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:20.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:20.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-16 19:55:20.109][biodb::testThat]
biodb.INFO [2025-04-16 19:55:20.110][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2025-04-16 19:55:20.111][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:55:20.112][biodb::testThat]
biodb.DEBUG[2025-04-16 19:55:20.115][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:20.118][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:55:20.119][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:55:20.120][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-16 19:55:20.550][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-16 19:55:20.903][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:55:20.905][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-04-16 19:55:20.909][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-04-16 19:55:20.911][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:20.912][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:20.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:20.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:20.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:20.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:20.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:20.928][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:20.932][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:55:20.932][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:55:20.934][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-16 19:55:21.266][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-16 19:55:21.649][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:55:21.652][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-04-16 19:55:21.669][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-04-16 19:55:21.671][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:21.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:21.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:21.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:21.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:21.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:21.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-16 19:55:21.691][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-16 19:55:21.693][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-16 19:55:21.694][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-16 19:55:21.695][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-16 19:55:21.696][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:21.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:21.697][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:21.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:21.699][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:21.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-16 19:55:21.712][biodb::testContext]
biodb.INFO [2025-04-16 19:55:21.713][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-16 19:55:21.715][biodb::testContext] Test context - Test web services
biodb.INFO [2025-04-16 19:55:21.716][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-16 19:55:21.718][biodb::testContext]
biodb.INFO [2025-04-16 19:55:21.849][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-16 19:55:21.852][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-16 19:55:21.872][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-16 19:55:21.873][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-16 19:55:21.874][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-16 19:55:21.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:21.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:21.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:21.877][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-16 19:55:21.879][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-16 19:55:21.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:21.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:21.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:21.884][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-16 19:55:21.885][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-16 19:55:21.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:21.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:21.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:21.898][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-16 19:55:21.899][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-16 19:55:21.900][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-16 19:55:21.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:21.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:21.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:21.903][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-16 19:55:21.904][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-16 19:55:21.905][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-16 19:55:21.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:21.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:21.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:21.910][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-16 19:55:21.911][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-16 19:55:21.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:21.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:21.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:21.917][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-16 19:55:21.919][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-16 19:55:21.920][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-16 19:55:21.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:21.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:21.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:21.924][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-16 19:55:21.926][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-16 19:55:21.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:21.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:21.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:21.931][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-16 19:55:21.932][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-16 19:55:21.933][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-16 19:55:21.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:21.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:21.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:21.941][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-16 19:55:21.942][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-16 19:55:21.944][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-16 19:55:21.945][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-16 19:55:21.946][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-16 19:55:21.947][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-16 19:55:21.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:21.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:21.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:21.950][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-16 19:55:21.950][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-16 19:55:21.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:21.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:21.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:21.955][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-16 19:55:21.956][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-16 19:55:21.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:21.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:21.960][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[2025-04-16 19:55:21.962][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-16 19:55:21.963][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-16 19:55:21.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:21.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:21.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:21.970][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-16 19:55:21.979][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-16 19:55:21.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:21.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:21.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:21.984][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-16 19:55:21.986][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-16 19:55:21.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:21.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:21.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:21.994][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-16 19:55:21.996][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-16 19:55:22.173][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-16 19:55:22.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:22.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:22.177][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[2025-04-16 19:55:22.179][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-16 19:55:22.180][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-16 19:55:22.182][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-16 19:55:22.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:22.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:22.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:22.199][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-16 19:55:22.201][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:22.209][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-16 19:55:22.211][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:22.213][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-16 19:55:22.214][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:22.216][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-16 19:55:22.217][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:22.219][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-16 19:55:22.224][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-16 19:55:22.226][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-16 19:55:22.228][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:22.230][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-16 19:55:22.231][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-16 19:55:22.233][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:22.241][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:22.245][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-16 19:55:22.245][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-16 19:55:22.245][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-16 19:55:22.245][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-16 19:55:22.245][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-16 19:55:22.249][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-16 19:55:22.251][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:22.252][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:22.260][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-16 19:55:22.262][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:22.263][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:22.265][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-16 19:55:22.266][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:22.268][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-16 19:55:22.277][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-16 19:55:22.280][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:22.281][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:22.283][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-16 19:55:22.286][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:22.296][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-16 19:55:22.298][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:22.300][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-16 19:55:22.301][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:22.303][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-16 19:55:22.304][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:22.310][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-16 19:55:22.312][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-16 19:55:22.313][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-16 19:55:22.315][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:22.317][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-16 19:55:22.318][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-16 19:55:22.327][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:22.330][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:22.332][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-16 19:55:22.332][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-16 19:55:22.332][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-16 19:55:22.332][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-16 19:55:22.332][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-16 19:55:22.335][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-16 19:55:22.336][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:22.338][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:22.339][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-16 19:55:22.341][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:22.342][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:22.343][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-16 19:55:22.350][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:22.352][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-16 19:55:22.353][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-16 19:55:22.355][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:22.356][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:22.358][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-16 19:55:22.368][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:22.369][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-16 19:55:22.371][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:22.372][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-16 19:55:22.374][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:22.376][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-16 19:55:22.383][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:22.385][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-16 19:55:22.386][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-16 19:55:22.388][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-16 19:55:22.389][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:22.391][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-16 19:55:22.400][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-16 19:55:22.401][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:22.403][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:22.405][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:22.406][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-16 19:55:22.407][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:22.416][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:22.418][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-16 19:55:22.419][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:22.421][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:22.422][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-16 19:55:22.423][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:22.425][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-16 19:55:22.432][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-16 19:55:22.434][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:22.435][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:22.437][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-16 19:55:22.439][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:22.447][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-16 19:55:22.449][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:22.451][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-16 19:55:22.453][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:22.455][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-16 19:55:22.456][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:22.458][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-16 19:55:22.468][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-16 19:55:22.470][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-16 19:55:22.472][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:22.474][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-16 19:55:22.475][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-16 19:55:22.477][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:22.487][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:22.489][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:22.491][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-16 19:55:22.492][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:22.494][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:22.495][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-16 19:55:22.505][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:22.507][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:22.508][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-16 19:55:22.510][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:22.512][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-16 19:55:22.513][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-16 19:55:22.521][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:22.523][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:22.525][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-16 19:55:22.526][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:22.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:22.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:22.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:22.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:22.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:22.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:22.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:22.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:22.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:22.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:22.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:22.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:22.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:22.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:22.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:22.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:22.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:22.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:22.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:22.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:22.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:22.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:22.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:22.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:22.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:22.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:22.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:22.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:22.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:22.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:22.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:22.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:22.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:22.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:22.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:22.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:22.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:22.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:22.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:22.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:22.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:22.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:22.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:22.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:22.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:22.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:22.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:22.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:22.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:22.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:22.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:22.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:22.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:22.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:22.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:22.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:22.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:22.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:22.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:22.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:22.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:22.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:22.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:22.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:22.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:22.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:22.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:22.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:22.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:22.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:22.703][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.DEBUG[2025-04-16 19:55:22.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:22.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:22.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:22.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:22.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:22.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:22.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:22.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:22.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:22.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:22.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:22.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:22.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:22.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:22.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:22.752][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-16 19:55:22.754][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-16 19:55:22.756][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-16 19:55:22.765][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-16 19:55:22.768][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-16 19:55:22.772][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-16 19:55:22.774][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-16 19:55:22.785][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-16 19:55:22.787][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-16 19:55:22.790][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-16 19:55:22.792][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-16 19:55:22.794][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-16 19:55:22.799][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-16 19:55:22.801][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-16 19:55:22.803][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-16 19:55:22.805][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-16 19:55:22.808][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-16 19:55:22.810][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-16 19:55:22.812][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-16 19:55:22.823][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-16 19:55:22.826][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-16 19:55:22.828][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-16 19:55:22.831][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-16 19:55:22.849][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-16 19:55:22.852][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-16 19:55:22.856][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-16 19:55:22.859][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-16 19:55:22.868][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-16 19:55:22.871][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-16 19:55:22.873][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-16 19:55:22.887][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-16 19:55:22.889][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-16 19:55:22.900][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-16 19:55:22.903][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-16 19:55:22.905][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-16 19:55:22.907][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-16 19:55:22.914][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-16 19:55:22.917][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-16 19:55:22.919][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-16 19:55:22.921][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-16 19:55:22.930][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-16 19:55:22.933][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-16 19:55:22.936][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-16 19:55:22.938][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-16 19:55:22.947][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-16 19:55:22.950][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-16 19:55:22.952][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-16 19:55:22.956][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-16 19:55:22.964][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-16 19:55:22.968][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-16 19:55:22.970][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-16 19:55:22.972][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-16 19:55:22.980][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-16 19:55:22.983][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-16 19:55:22.985][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-16 19:55:22.987][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-16 19:55:22.989][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-16 19:55:22.999][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-16 19:55:23.001][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-16 19:55:23.004][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-16 19:55:23.006][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-16 19:55:23.008][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-16 19:55:23.010][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-16 19:55:23.019][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-16 19:55:23.022][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-16 19:55:23.024][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-16 19:55:23.029][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-16 19:55:23.032][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-16 19:55:23.035][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-16 19:55:23.037][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-16 19:55:23.039][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-16 19:55:23.043][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-16 19:55:23.045][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-16 19:55:23.046][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-16 19:55:23.048][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-16 19:55:23.049][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-16 19:55:23.050][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-16 19:55:23.051][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-16 19:55:23.053][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-16 19:55:23.056][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-16 19:55:23.058][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-16 19:55:23.060][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-16 19:55:23.062][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-16 19:55:23.064][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-16 19:55:23.066][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-16 19:55:23.067][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-16 19:55:23.069][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:23.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:23.072][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:23.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:23.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:23.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:23.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:23.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:23.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:23.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:23.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:23.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:23.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:23.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:23.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:23.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:23.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:23.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:23.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:23.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:23.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:23.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:23.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:23.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:23.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:23.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:23.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:23.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:23.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:23.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:23.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:23.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:23.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:23.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:23.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:23.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:23.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:23.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:23.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:23.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:23.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:23.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:23.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:23.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:23.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:23.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:23.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:23.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:23.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:23.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:23.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:23.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:23.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:23.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:23.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:23.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:23.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:23.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:23.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:23.144][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[2025-04-16 19:55:23.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:23.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:23.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:23.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:23.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:23.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:23.151][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[2025-04-16 19:55:23.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:23.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:23.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:23.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:23.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:23.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:23.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:23.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:23.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:23.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:23.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:23.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:23.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:23.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:23.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:23.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:23.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:23.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:23.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:23.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:23.179][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[2025-04-16 19:55:23.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:23.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:23.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:23.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:23.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:23.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:23.187][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[2025-04-16 19:55:23.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:23.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:23.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:23.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:23.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:23.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:23.194][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[2025-04-16 19:55:23.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:23.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:23.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:23.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:23.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:23.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:23.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:23.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:23.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:23.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:23.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:23.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:23.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:23.219][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[2025-04-16 19:55:23.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:23.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:23.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:23.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:23.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:23.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:23.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:23.249][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-16 19:55:23.251][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-16 19:55:23.253][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:23.255][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-16 19:55:23.256][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:23.257][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-16 19:55:23.258][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:23.258][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-16 19:55:23.259][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:23.260][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-16 19:55:23.261][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-16 19:55:23.262][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-16 19:55:23.263][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:23.264][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-16 19:55:23.265][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-16 19:55:23.276][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-16 19:55:23.276][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-16 19:55:23.276][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-16 19:55:23.276][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-16 19:55:23.276][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-16 19:55:23.276][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-16 19:55:23.276][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-16 19:55:23.276][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-16 19:55:23.276][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-16 19:55:23.276][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-16 19:55:23.276][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-16 19:55:23.277][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:23.278][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-16 19:55:23.278][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-16 19:55:23.278][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-16 19:55:23.279][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-16 19:55:23.291][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:23.293][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:23.294][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-16 19:55:23.295][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:23.297][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:23.298][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-16 19:55:23.299][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:55:23.299][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-16 19:55:23.301][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-16 19:55:23.302][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-16 19:55:23.302][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:23.315][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-16 19:55:23.315][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-16 19:55:23.317][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-16 19:55:23.319][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-16 19:55:23.322][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-16 19:55:23.324][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-16 19:55:23.326][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-16 19:55:23.327][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-16 19:55:23.330][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-16 19:55:23.331][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-16 19:55:23.333][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-16 19:55:23.335][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-16 19:55:23.336][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-16 19:55:23.339][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-16 19:55:23.341][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-16 19:55:23.342][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-16 19:55:23.343][biodb::testThat]
biodb.INFO [2025-04-16 19:55:23.344][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-04-16 19:55:23.344][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:55:23.345][biodb::testThat]
biodb.DEBUG[2025-04-16 19:55:23.348][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-16 19:55:23.354][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-16 19:55:23.356][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-04-16 19:55:23.357][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-16 19:55:23.358][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-04-16 19:55:23.362][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:23.366][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:55:23.367][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:55:23.368][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-16 19:55:23.715][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-16 19:55:24.059][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:55:24.063][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-04-16 19:55:24.069][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-04-16 19:55:24.085][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-16 19:55:24.087][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-16 19:55:24.089][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-16 19:55:24.091][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-16 19:55:24.092][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:24.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:24.095][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:24.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:24.098][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-16 19:55:24.106][biodb::testContext]
biodb.INFO [2025-04-16 19:55:24.108][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-16 19:55:24.110][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-04-16 19:55:24.111][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-16 19:55:24.113][biodb::testContext]
biodb.INFO [2025-04-16 19:55:24.116][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-16 19:55:24.119][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-16 19:55:24.126][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-16 19:55:24.128][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-16 19:55:24.130][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-16 19:55:24.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.136][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-16 19:55:24.137][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-16 19:55:24.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.143][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-16 19:55:24.145][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-16 19:55:24.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.150][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-16 19:55:24.151][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-16 19:55:24.153][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-16 19:55:24.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.158][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-16 19:55:24.160][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-16 19:55:24.162][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-16 19:55:24.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.167][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-16 19:55:24.169][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-16 19:55:24.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.174][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-16 19:55:24.176][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-16 19:55:24.177][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-16 19:55:24.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.200][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[2025-04-16 19:55:24.203][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-16 19:55:24.205][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-16 19:55:24.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.218][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-16 19:55:24.220][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-16 19:55:24.222][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-16 19:55:24.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.234][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-16 19:55:24.236][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-16 19:55:24.238][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-16 19:55:24.240][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-16 19:55:24.242][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-16 19:55:24.252][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-16 19:55:24.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.260][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-16 19:55:24.269][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-16 19:55:24.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.276][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-16 19:55:24.278][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-16 19:55:24.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.293][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-16 19:55:24.296][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-16 19:55:24.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.308][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[2025-04-16 19:55:24.310][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-16 19:55:24.312][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-16 19:55:24.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.325][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-16 19:55:24.327][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-16 19:55:24.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.341][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-16 19:55:24.343][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-16 19:55:24.592][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-16 19:55:24.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.598][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-16 19:55:24.599][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-16 19:55:24.601][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-16 19:55:24.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.605][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-16 19:55:24.606][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:24.608][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-16 19:55:24.609][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:24.610][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-16 19:55:24.611][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:24.612][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-16 19:55:24.613][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:24.614][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-16 19:55:24.614][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-16 19:55:24.615][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-16 19:55:24.616][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:24.617][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-16 19:55:24.618][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-16 19:55:24.619][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:24.619][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:24.620][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-16 19:55:24.620][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-16 19:55:24.620][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-16 19:55:24.620][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-16 19:55:24.620][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-16 19:55:24.624][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-16 19:55:24.626][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:24.627][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:24.628][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-16 19:55:24.629][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:24.631][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:24.631][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-16 19:55:24.632][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:24.633][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-16 19:55:24.634][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-16 19:55:24.636][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:24.636][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:24.637][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-16 19:55:24.639][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:24.640][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-16 19:55:24.640][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:24.641][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-16 19:55:24.642][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:24.653][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-16 19:55:24.655][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:24.657][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-16 19:55:24.658][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-16 19:55:24.659][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-16 19:55:24.660][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:24.662][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-16 19:55:24.663][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-16 19:55:24.665][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:24.666][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:24.667][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-16 19:55:24.667][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-16 19:55:24.667][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-16 19:55:24.667][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-16 19:55:24.667][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-16 19:55:24.668][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-16 19:55:24.669][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:24.670][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:24.671][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-16 19:55:24.672][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:24.673][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:24.674][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-16 19:55:24.675][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:24.676][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-16 19:55:24.676][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-16 19:55:24.678][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:24.679][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:24.681][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-16 19:55:24.683][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:24.684][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-16 19:55:24.686][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:24.687][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-16 19:55:24.688][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:24.690][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-16 19:55:24.691][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:24.693][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-16 19:55:24.694][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-16 19:55:24.695][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-16 19:55:24.696][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:24.697][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-16 19:55:24.699][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-16 19:55:24.700][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:24.701][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:24.702][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:24.704][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-16 19:55:24.705][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:24.706][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:24.707][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-16 19:55:24.708][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:24.720][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:24.721][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-16 19:55:24.723][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:24.724][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-16 19:55:24.725][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-16 19:55:24.727][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:24.741][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:24.743][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-16 19:55:24.746][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:24.747][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-16 19:55:24.749][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:24.750][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-16 19:55:24.751][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:24.752][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-16 19:55:24.754][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:24.755][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-16 19:55:24.755][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-16 19:55:24.757][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-16 19:55:24.758][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:24.759][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-16 19:55:24.760][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-16 19:55:24.761][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:24.762][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:24.763][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:24.765][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-16 19:55:24.766][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:24.766][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:24.767][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-16 19:55:24.768][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:24.769][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:24.770][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-16 19:55:24.770][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:24.771][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-16 19:55:24.772][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-16 19:55:24.774][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:24.775][self$setPropertyValue]
biodb.DEBUG[2025-04-16 19:55:24.776][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-16 19:55:24.777][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.778][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[2025-04-16 19:55:24.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:24.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:24.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:24.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:24.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.785][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[2025-04-16 19:55:24.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:24.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:24.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:24.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:24.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:24.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:24.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:24.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:24.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.814][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[2025-04-16 19:55:24.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:24.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:24.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:24.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:24.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.832][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[2025-04-16 19:55:24.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:24.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:24.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:24.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:24.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.841][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[2025-04-16 19:55:24.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:24.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:24.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.846][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[2025-04-16 19:55:24.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:24.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:24.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:24.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:24.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:24.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:24.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.857][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[2025-04-16 19:55:24.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:24.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:24.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:24.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:24.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:24.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:24.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:24.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:24.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:24.870][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-16 19:55:24.872][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-16 19:55:24.873][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-16 19:55:24.874][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-16 19:55:24.876][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-16 19:55:24.877][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-16 19:55:24.878][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-16 19:55:24.879][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-16 19:55:24.880][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-16 19:55:24.892][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-16 19:55:24.893][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-16 19:55:24.895][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-16 19:55:24.896][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-16 19:55:24.897][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-16 19:55:24.898][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-16 19:55:24.899][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-16 19:55:24.900][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-16 19:55:24.902][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-16 19:55:24.903][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-16 19:55:24.905][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-16 19:55:24.906][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-16 19:55:24.907][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-16 19:55:24.908][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-16 19:55:24.909][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-16 19:55:24.910][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-16 19:55:24.911][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-16 19:55:24.912][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-16 19:55:24.913][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-16 19:55:24.914][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-16 19:55:24.916][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-16 19:55:24.917][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-16 19:55:24.918][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-16 19:55:24.919][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-16 19:55:24.921][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-16 19:55:24.922][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-16 19:55:24.923][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-16 19:55:24.924][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-16 19:55:24.925][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-16 19:55:24.926][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-16 19:55:24.928][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-16 19:55:24.929][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-16 19:55:24.930][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-16 19:55:24.931][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-16 19:55:24.932][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-16 19:55:24.934][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-16 19:55:24.935][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-16 19:55:24.936][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-16 19:55:24.937][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-16 19:55:24.949][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-16 19:55:24.951][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-16 19:55:24.952][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-16 19:55:24.953][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-16 19:55:24.954][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-16 19:55:24.955][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-16 19:55:24.957][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-16 19:55:24.958][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-16 19:55:24.963][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-16 19:55:24.964][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-16 19:55:24.965][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-16 19:55:24.966][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-16 19:55:24.968][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-16 19:55:24.969][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-16 19:55:24.970][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-16 19:55:24.971][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-16 19:55:24.972][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-16 19:55:24.973][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-16 19:55:24.974][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-16 19:55:24.975][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-16 19:55:24.976][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-16 19:55:24.976][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-16 19:55:24.978][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-16 19:55:24.979][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-16 19:55:24.979][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-16 19:55:24.981][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-16 19:55:24.982][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-16 19:55:24.983][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-16 19:55:24.984][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-16 19:55:24.985][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-16 19:55:24.997][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-16 19:55:24.999][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-16 19:55:25.000][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-16 19:55:25.001][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-16 19:55:25.002][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-16 19:55:25.003][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-16 19:55:25.004][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-16 19:55:25.005][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-16 19:55:25.006][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:25.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:25.008][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:25.008][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.DEBUG[2025-04-16 19:55:25.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:25.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:25.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:25.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:25.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:25.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:25.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:25.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:25.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:25.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:25.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:25.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:25.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:25.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:25.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:25.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:25.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:25.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:25.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:25.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:25.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:25.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:25.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:25.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:25.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:25.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:25.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:25.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:25.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:25.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:25.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:25.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:25.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:25.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:25.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:25.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:25.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:25.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:25.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:25.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:25.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:25.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:25.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:25.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:25.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:25.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:25.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:25.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:25.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:25.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:25.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:25.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:25.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:25.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:25.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:25.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:25.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:25.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:25.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:25.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:25.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:25.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:25.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:25.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:25.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:25.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:25.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:25.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:25.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:25.091][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[2025-04-16 19:55:25.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:25.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:25.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:25.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:25.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:25.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:25.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:25.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:25.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:25.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:25.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:25.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:25.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:25.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:25.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:25.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:25.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:25.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:25.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:25.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:25.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:25.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:25.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:25.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:25.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:25.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:25.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:25.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:25.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:25.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:25.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:25.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:25.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:25.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:25.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:25.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:25.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:25.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:25.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:25.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:25.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:25.154][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[2025-04-16 19:55:25.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-16 19:55:25.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:25.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:25.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:25.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:25.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:25.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:25.206][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-16 19:55:25.210][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-16 19:55:25.211][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:25.224][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-16 19:55:25.225][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:25.226][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-16 19:55:25.227][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:25.228][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-16 19:55:25.229][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:25.230][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-16 19:55:25.242][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-16 19:55:25.243][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-16 19:55:25.244][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:25.245][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-16 19:55:25.245][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-16 19:55:25.246][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-16 19:55:25.246][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-16 19:55:25.246][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-16 19:55:25.246][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-16 19:55:25.246][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-16 19:55:25.246][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-16 19:55:25.246][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-16 19:55:25.246][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-16 19:55:25.246][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-16 19:55:25.246][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-16 19:55:25.246][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-16 19:55:25.247][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-16 19:55:25.248][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-16 19:55:25.248][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-16 19:55:25.248][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-16 19:55:25.249][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-16 19:55:25.249][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:25.250][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:25.251][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-16 19:55:25.252][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-16 19:55:25.253][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-16 19:55:25.254][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-16 19:55:25.255][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:55:25.255][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-16 19:55:25.255][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-16 19:55:25.256][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-16 19:55:25.257][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-16 19:55:25.257][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-16 19:55:25.257][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-16 19:55:25.258][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-16 19:55:25.260][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-16 19:55:25.261][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-16 19:55:25.262][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-16 19:55:25.263][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-16 19:55:25.265][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-16 19:55:25.267][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-16 19:55:25.268][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-16 19:55:25.269][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-16 19:55:25.270][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-16 19:55:25.271][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-16 19:55:25.272][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-16 19:55:25.273][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-16 19:55:25.276][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-16 19:55:25.277][biodb::testThat]
biodb.INFO [2025-04-16 19:55:25.278][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-04-16 19:55:25.279][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-16 19:55:25.279][biodb::testThat]
biodb.DEBUG[2025-04-16 19:55:25.282][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-16 19:55:25.285][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-16 19:55:25.286][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-04-16 19:55:25.300][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-16 19:55:25.301][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-04-16 19:55:25.305][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-16 19:55:25.307][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-16 19:55:25.309][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-04-16 19:55:25.309][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-16 19:55:25.311][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-04-16 19:55:25.315][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-04-16 19:55:25.316][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-16 19:55:25.317][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-04-16 19:55:25.318][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-16 19:55:25.319][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-16 19:55:25.319][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-16 19:55:25.320][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-16 19:55:25.321][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-16 19:55:25.322][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-16 19:55:25.325][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:25.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:25.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:25.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:25.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:25.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:25.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-16 19:55:25.334][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-04-16 19:55:25.337][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-16 19:55:25.349][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-16 19:55:25.351][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-04-16 19:55:25.997][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-04-16 19:55:27.083][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-16 19:55:27.086][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-04-16 19:55:27.094][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-04-16 19:55:27.096][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-04-16 19:55:27.098][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-16 19:55:27.100][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-16 19:55:27.101][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-16 19:55:27.102][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-16 19:55:27.103][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:27.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:27.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:27.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:27.111][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:27.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-16 19:55:27.116][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:27.117][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:27.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.119][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:27.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:27.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.124][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:55:27.125][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:55:27.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.127][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.128][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-16 19:55:27.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-16 19:55:27.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.131][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:55:27.132][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:55:27.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.135][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.136][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-16 19:55:27.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-16 19:55:27.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.140][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-16 19:55:27.141][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-16 19:55:27.141][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.142][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.143][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-16 19:55:27.144][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-16 19:55:27.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.147][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.148][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:55:27.149][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:55:27.149][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.150][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.151][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:55:27.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-16 19:55:27.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.154][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:55:27.155][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:27.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.158][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.159][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-16 19:55:27.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-16 19:55:27.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.162][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:27.163][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:27.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.174][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:27.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-16 19:55:27.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.179][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:55:27.180][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:55:27.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.182][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.183][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-16 19:55:27.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-16 19:55:27.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.186][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:55:27.187][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:55:27.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.189][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.190][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-16 19:55:27.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-16 19:55:27.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.193][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:55:27.194][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:55:27.195][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.196][ef$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.197][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-16 19:55:27.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-16 19:55:27.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:27.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:27.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.203][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:27.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:27.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:27.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:27.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.210][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-16 19:55:27.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-16 19:55:27.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:27.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:27.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:27.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:27.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:27.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:27.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:27.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:27.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:27.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:27.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-16 19:55:27.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-16 19:55:27.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-16 19:55:27.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-16 19:55:27.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-16 19:55:27.234][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-04-16 19:55:27.238][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-16 19:55:27.239][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-16 19:55:27.241][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-16 19:55:27.241][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-16 19:55:27.242][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-16 19:55:27.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-16 19:55:27.243][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-16 19:55:27.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-16 19:55:27.245][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-16 19:55:27.246][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
> 
> proc.time()
   user  system elapsed 
 24.124   1.492  78.171

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn2.7651.1185.084
ChebiEntry0.3560.0150.388