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This page was generated on 2025-01-16 12:09 -0500 (Thu, 16 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4489
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4469
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4387
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 202/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.12.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-01-13 13:00 -0500 (Mon, 13 Jan 2025)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: RELEASE_3_20
git_last_commit: e6b963e
git_last_commit_date: 2024-10-29 11:04:35 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    NA  

CHECK results for biodbChebi on kjohnson1

To the developers/maintainers of the biodbChebi package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: biodbChebi
Version: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2025-01-14 12:34:51 -0500 (Tue, 14 Jan 2025)
EndedAt: 2025-01-14 12:36:15 -0500 (Tue, 14 Jan 2025)
EllapsedTime: 84.3 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.12.0’
* 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 2.688  1.144   5.149
* 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/4.4-arm64/Resources/library’
* installing *source* package ‘biodbChebi’ ...
** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2025-01-14 12:35:42.532][biodb::testContext]
biodb.INFO [2025-01-14 12:35:42.538][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-14 12:35:42.539][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-01-14 12:35:42.540][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-14 12:35:42.541][biodb::testContext]
biodb.INFO [2025-01-14 12:35:42.551][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-14 12:35:42.553][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-01-14 12:35:42.564][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-14 12:35:42.565][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-14 12:35:42.566][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-14 12:35:42.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.570][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-14 12:35:42.591][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-14 12:35:42.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.595][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-14 12:35:42.597][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-14 12:35:42.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.600][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-14 12:35:42.620][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-14 12:35:42.621][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-14 12:35:42.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.625][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-14 12:35:42.626][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-14 12:35:42.627][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-14 12:35:42.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.631][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-14 12:35:42.632][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-14 12:35:42.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.636][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-14 12:35:42.636][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-14 12:35:42.637][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-14 12:35:42.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.640][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-14 12:35:42.641][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-14 12:35:42.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.644][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-14 12:35:42.645][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-14 12:35:42.646][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-14 12:35:42.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.649][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-14 12:35:42.650][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-14 12:35:42.651][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-14 12:35:42.652][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-14 12:35:42.653][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-14 12:35:42.654][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-14 12:35:42.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.658][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-14 12:35:42.660][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-14 12:35:42.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.664][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-14 12:35:42.666][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-14 12:35:42.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.670][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-14 12:35:42.671][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-14 12:35:42.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.674][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-14 12:35:42.675][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-14 12:35:42.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.678][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-14 12:35:42.679][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-14 12:35:42.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.683][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-14 12:35:42.684][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-14 12:35:42.707][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-14 12:35:42.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.711][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-14 12:35:42.712][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-14 12:35:42.713][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-14 12:35:42.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.722][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-14 12:35:42.758][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-14 12:35:42.774][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-14 12:35:42.775][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-14 12:35:42.776][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-14 12:35:42.777][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-14 12:35:42.778][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-14 12:35:42.779][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-14 12:35:42.780][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-14 12:35:42.781][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-14 12:35:42.782][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-14 12:35:42.782][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-14 12:35:42.783][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-14 12:35:42.784][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-14 12:35:42.785][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:35:42.786][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-14 12:35:42.787][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-14 12:35:42.787][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-14 12:35:42.787][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-14 12:35:42.787][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-14 12:35:42.787][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-14 12:35:42.788][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-14 12:35:42.789][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:35:42.790][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:35:42.791][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-14 12:35:42.792][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:35:42.793][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:35:42.793][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-14 12:35:42.794][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:35:42.795][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-14 12:35:42.796][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-14 12:35:42.797][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-14 12:35:42.798][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:35:42.799][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-14 12:35:42.801][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-14 12:35:42.802][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-14 12:35:42.803][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-14 12:35:42.804][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-14 12:35:42.805][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-14 12:35:42.806][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-14 12:35:42.807][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-14 12:35:42.808][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-14 12:35:42.809][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-14 12:35:42.810][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-14 12:35:42.811][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-14 12:35:42.812][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-14 12:35:42.812][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-14 12:35:42.813][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:35:42.814][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-14 12:35:42.815][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-14 12:35:42.815][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-14 12:35:42.815][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-14 12:35:42.815][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-14 12:35:42.815][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-14 12:35:42.816][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-14 12:35:42.817][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:35:42.818][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:35:42.819][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-14 12:35:42.819][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:35:42.820][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:35:42.821][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-14 12:35:42.822][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:35:42.823][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-14 12:35:42.823][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-14 12:35:42.824][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-14 12:35:42.825][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:35:42.826][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-14 12:35:42.828][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-14 12:35:42.829][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-14 12:35:42.830][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-14 12:35:42.831][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-14 12:35:42.832][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-14 12:35:42.833][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-14 12:35:42.841][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-14 12:35:42.842][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-14 12:35:42.843][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-14 12:35:42.843][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-14 12:35:42.844][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-14 12:35:42.845][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-14 12:35:42.846][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-14 12:35:42.847][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:35:42.847][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-14 12:35:42.848][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:35:42.849][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-14 12:35:42.850][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:35:42.851][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:35:42.851][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-14 12:35:42.852][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:35:42.853][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:35:42.854][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-14 12:35:42.854][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:35:42.855][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-14 12:35:42.856][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-14 12:35:42.857][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-14 12:35:42.857][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:35:42.858][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-14 12:35:42.860][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-14 12:35:42.861][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-14 12:35:42.862][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-14 12:35:42.862][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-14 12:35:42.863][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-14 12:35:42.864][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-14 12:35:42.865][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-14 12:35:42.866][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-14 12:35:42.866][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-14 12:35:42.867][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-14 12:35:42.868][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-14 12:35:42.869][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-14 12:35:42.870][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-14 12:35:42.870][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:35:42.871][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-14 12:35:42.872][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:35:42.873][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-14 12:35:42.874][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:35:42.874][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:35:42.875][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-14 12:35:42.876][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:35:42.877][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:35:42.878][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-14 12:35:42.878][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:35:42.879][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-14 12:35:42.880][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-14 12:35:42.881][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-14 12:35:42.881][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:35:42.887][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-14 12:35:42.888][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:42.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:42.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:42.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:42.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:42.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:42.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:42.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:42.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:42.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:42.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:42.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:42.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:42.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:42.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:42.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:42.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:42.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:42.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:42.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:42.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.925][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[2025-01-14 12:35:42.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:42.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:42.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.930][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[2025-01-14 12:35:42.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:42.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:42.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:42.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:42.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:42.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:42.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:42.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:42.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:42.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:42.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:42.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:42.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:42.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:42.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:42.955][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-14 12:35:42.962][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-14 12:35:42.963][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-14 12:35:42.965][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-14 12:35:42.966][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-14 12:35:42.967][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-14 12:35:42.968][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-14 12:35:42.970][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-14 12:35:42.971][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-14 12:35:42.972][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-14 12:35:42.973][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-14 12:35:42.975][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-14 12:35:42.976][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-14 12:35:42.977][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-14 12:35:42.978][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-14 12:35:42.980][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-14 12:35:42.981][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-14 12:35:42.982][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-14 12:35:42.984][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-14 12:35:42.985][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-14 12:35:42.986][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-14 12:35:42.988][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-14 12:35:42.989][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-14 12:35:42.990][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-14 12:35:42.992][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-14 12:35:42.993][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-14 12:35:42.994][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-14 12:35:42.995][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-14 12:35:42.997][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-14 12:35:42.998][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-14 12:35:42.999][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-14 12:35:43.000][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-14 12:35:43.001][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-14 12:35:43.003][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-14 12:35:43.004][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-14 12:35:43.005][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-14 12:35:43.006][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-14 12:35:43.007][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-14 12:35:43.009][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-14 12:35:43.010][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-14 12:35:43.011][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-14 12:35:43.012][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-14 12:35:43.020][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-14 12:35:43.021][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-14 12:35:43.023][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-14 12:35:43.024][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-14 12:35:43.025][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-14 12:35:43.026][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-14 12:35:43.028][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-14 12:35:43.029][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-14 12:35:43.030][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-14 12:35:43.032][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-14 12:35:43.033][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-14 12:35:43.035][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-14 12:35:43.036][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-14 12:35:43.037][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-14 12:35:43.038][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-14 12:35:43.040][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-14 12:35:43.041][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-14 12:35:43.042][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-14 12:35:43.043][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-14 12:35:43.044][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-14 12:35:43.045][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-14 12:35:43.047][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-14 12:35:43.048][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-14 12:35:43.049][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-14 12:35:43.050][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-14 12:35:43.051][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-14 12:35:43.052][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-14 12:35:43.054][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-14 12:35:43.055][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-14 12:35:43.056][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-14 12:35:43.057][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-14 12:35:43.058][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-14 12:35:43.059][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-14 12:35:43.060][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-14 12:35:43.062][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-14 12:35:43.063][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-14 12:35:43.064][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-14 12:35:43.065][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-14 12:35:43.066][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-14 12:35:43.067][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-14 12:35:43.068][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-14 12:35:43.074][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-14 12:35:43.076][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-14 12:35:43.081][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-14 12:35:43.082][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:43.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:43.083][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:43.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:43.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:43.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:43.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:43.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:43.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:43.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:43.095][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[2025-01-14 12:35:43.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:43.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:43.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:43.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:43.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:43.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:43.100][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[2025-01-14 12:35:43.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:43.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:43.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:43.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:43.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:43.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:43.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:43.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:43.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:43.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:43.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:43.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:43.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:43.110][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[2025-01-14 12:35:43.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:43.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:43.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:43.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:43.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:43.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:43.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:43.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:43.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:43.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:43.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:43.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:43.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:43.119][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[2025-01-14 12:35:43.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:43.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:43.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:43.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:43.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:43.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:43.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:43.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:43.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:43.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:43.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:43.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:43.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:43.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:43.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:43.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:43.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:43.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:43.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:43.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:43.134][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[2025-01-14 12:35:43.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:43.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:43.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:43.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:43.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:43.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:43.139][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[2025-01-14 12:35:43.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:43.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:43.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:43.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:43.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:43.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:43.144][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[2025-01-14 12:35:43.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:43.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:43.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:43.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:43.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:43.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:43.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:43.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:43.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:43.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:43.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:43.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:43.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:43.154][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[2025-01-14 12:35:43.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:43.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:43.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:43.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:43.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:43.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:43.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:43.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:43.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:43.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:43.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:43.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:43.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:43.164][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[2025-01-14 12:35:43.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:43.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:43.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:43.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:43.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:43.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:43.169][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[2025-01-14 12:35:43.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:35:43.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:43.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:43.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:43.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:43.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:43.174][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[2025-01-14 12:35:43.177][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-01-14 12:35:43.193][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-01-14 12:35:43.195][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-14 12:35:43.196][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-14 12:35:43.197][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-14 12:35:43.198][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-14 12:35:43.199][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-14 12:35:43.200][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-14 12:35:43.201][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-14 12:35:43.201][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-01-14 12:35:43.202][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-14 12:35:43.203][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-14 12:35:43.204][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-14 12:35:43.205][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-01-14 12:35:43.206][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-14 12:35:43.207][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-01-14 12:35:43.207][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-01-14 12:35:43.207][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-01-14 12:35:43.207][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-01-14 12:35:43.207][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-01-14 12:35:43.207][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-01-14 12:35:43.207][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-01-14 12:35:43.207][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-01-14 12:35:43.207][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-01-14 12:35:43.207][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-01-14 12:35:43.207][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-01-14 12:35:43.208][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-14 12:35:43.208][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-14 12:35:43.208][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-14 12:35:43.208][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-14 12:35:43.209][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-14 12:35:43.210][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:35:43.211][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:35:43.212][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-14 12:35:43.212][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:35:43.213][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:35:43.214][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-14 12:35:43.215][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:43.215][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-01-14 12:35:43.216][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-14 12:35:43.216][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-14 12:35:43.217][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-14 12:35:43.218][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-01-14 12:35:43.218][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-01-14 12:35:43.224][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-14 12:35:43.226][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-14 12:35:43.228][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-01-14 12:35:43.229][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-14 12:35:43.231][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-14 12:35:43.233][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-14 12:35:43.266][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-01-14 12:35:43.267][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-01-14 12:35:43.273][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-01-14 12:35:43.278][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-01-14 12:35:43.284][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-14 12:35:43.285][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-14 12:35:43.286][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-01-14 12:35:43.287][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-01-14 12:35:43.300][biodb::testThat]
biodb.INFO [2025-01-14 12:35:43.301][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-01-14 12:35:43.302][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:35:43.303][biodb::testThat]
biodb.TRACE[2025-01-14 12:35:43.308][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-01-14 12:35:43.311][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:43.316][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:43.328][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:43.329][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:43.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:43.346][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:43.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:43.348][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:43.349][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[2025-01-14 12:35:43.362][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:43.363][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:43.364][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.365][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:43.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:43.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.383][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:43.384][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:43.385][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.386][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.413][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:43.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:43.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.417][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:43.418][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:43.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.432][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.434][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:43.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:43.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.437][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:43.438][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:43.439][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.440][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.441][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:43.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:43.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.444][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:43.445][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:43.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.447][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.448][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:43.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:43.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.452][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:43.453][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:43.454][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.455][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.456][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:43.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:43.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.460][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:43.460][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:43.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.462][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.463][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:43.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:43.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.467][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:43.468][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:43.469][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.469][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:43.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:43.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.474][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:43.475][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:43.476][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.476][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.478][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:43.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:43.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.481][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:43.482][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:43.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.484][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.485][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:43.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:43.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.488][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:43.489][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:43.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.491][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.492][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:43.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:43.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:43.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:43.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:43.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:43.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:43.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:43.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:43.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:43.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:43.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:43.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:43.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:43.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:43.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:43.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:43.564][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-01-14 12:35:43.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:43.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:43.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.619][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:43.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:43.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.647][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:43.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:43.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.651][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:43.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:43.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.654][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:43.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:43.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.658][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:43.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:43.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.661][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-14 12:35:43.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-14 12:35:43.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.665][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-14 12:35:43.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-14 12:35:43.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.668][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-14 12:35:43.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-14 12:35:43.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.671][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-14 12:35:43.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-14 12:35:43.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:43.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:43.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.715][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:43.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:43.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:43.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:43.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:43.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:43.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:43.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:43.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:43.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:43.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:43.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:43.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.749][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:43.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:43.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:43.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:43.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:43.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:43.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.783][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:43.784][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:43.785][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.786][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:43.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:43.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.800][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.803][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.810][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.811][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.812][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:43.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.825][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:43.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:43.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.829][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:43.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:43.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.832][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:43.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:43.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.835][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:43.836][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:43.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.838][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.839][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:43.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:43.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.851][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:43.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:43.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.855][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:43.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:43.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.858][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:43.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:43.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.861][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:43.862][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:43.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.864][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.865][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:43.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:43.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:43.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:43.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.882][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:43.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:43.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:43.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:43.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.888][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:43.889][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:43.890][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.891][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:43.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:43.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.904][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:43.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:43.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:43.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:43.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:43.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:43.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.915][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:43.916][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:43.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.917][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:43.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:43.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.929][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:43.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:43.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.933][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:43.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:43.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.943][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:43.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:43.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.946][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:43.947][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:43.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.949][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.950][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:43.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:43.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.961][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-14 12:35:43.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:43.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.965][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-14 12:35:43.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:43.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.968][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-14 12:35:43.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:43.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.972][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-14 12:35:43.972][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:43.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.974][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.975][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-14 12:35:43.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:43.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.987][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:43.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:43.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.992][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:43.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:43.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.995][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:43.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:43.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:43.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:43.999][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:44.000][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:44.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.002][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.002][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:44.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:44.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.014][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:44.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:44.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.018][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:44.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:44.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.021][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:44.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:44.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.025][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:44.026][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:44.026][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.027][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.028][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:44.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:44.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.039][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:44.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:44.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.044][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:44.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:44.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.047][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:44.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:44.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.051][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:44.051][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:44.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.053][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.054][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:44.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:44.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.065][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:44.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:44.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.069][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:44.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:44.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.073][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:44.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:44.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.076][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:44.077][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:44.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.078][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.079][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:44.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:44.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.098][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:44.100][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:44.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.101][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.106][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:44.108][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:44.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.109][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.114][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:44.115][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:44.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.117][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.122][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:44.123][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:44.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.124][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.129][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:44.130][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:44.131][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.132][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.137][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:44.139][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:44.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.141][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.146][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:44.148][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:44.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.149][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.154][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:44.156][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:44.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.157][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.163][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-14 12:35:44.164][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:44.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.165][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.171][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:44.172][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:44.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.174][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.178][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:44.180][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:44.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.181][ef$get] fields variable is a list.
biodb.INFO [2025-01-14 12:35:44.191][biodb::testThat]
biodb.INFO [2025-01-14 12:35:44.192][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-01-14 12:35:44.193][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:35:44.193][biodb::testThat]
biodb.DEBUG[2025-01-14 12:35:44.208][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-01-14 12:35:44.218][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:44.222][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-01-14 12:35:44.224][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:35:44.225][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-01-14 12:35:44.226][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:44.250][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:44.251][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:44.253][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:44.254][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:44.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:44.260][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:44.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:44.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:44.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:44.273][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:44.274][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:44.275][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.276][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:44.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:44.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.297][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:44.298][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:44.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.300][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.301][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:44.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:44.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.305][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:44.306][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:44.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.307][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.308][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:44.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:44.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.312][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:44.313][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:44.313][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.314][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.315][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:44.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:44.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.319][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:44.319][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:44.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.321][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.322][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:44.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:44.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.325][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:44.326][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:44.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.328][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.329][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:44.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:44.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.332][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:44.333][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:44.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.334][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.335][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:44.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:44.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.339][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:44.340][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:44.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.342][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:44.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:44.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.346][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:44.347][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:44.348][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.349][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.350][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:44.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:44.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.354][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:44.355][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:44.356][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.357][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.358][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:44.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:44.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.361][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:44.362][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:44.363][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.364][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.365][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:44.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:44.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:44.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:44.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:44.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:44.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:44.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:44.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:44.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:44.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:44.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:44.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:44.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:44.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:44.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:44.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:44.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:44.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:44.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:44.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:44.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:44.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:44.407][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-01-14 12:35:44.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-01-14 12:35:44.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-01-14 12:35:44.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-01-14 12:35:44.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-01-14 12:35:44.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-01-14 12:35:44.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-01-14 12:35:44.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-14 12:35:44.426][biodb::testThat]
biodb.INFO [2025-01-14 12:35:44.427][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-01-14 12:35:44.428][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:35:44.429][biodb::testThat]
biodb.TRACE[2025-01-14 12:35:44.432][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:44.433][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:44.434][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.435][ef$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:44.436][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-01-14 12:35:44.464][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:44.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:44.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.469][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:44.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:44.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:44.472][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:44.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:44.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:44.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:44.478][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-01-14 12:35:44.484][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-01-14 12:35:44.506][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:35:44.523][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-01-14 12:35:44.525][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:35:44.526][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-01-14 12:35:44.557][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[2025-01-14 12:35:44.561][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:44.562][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:44.564][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-01-14 12:35:44.958][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-01-14 12:35:45.227][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:45.229][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-01-14 12:35:45.245][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-01-14 12:35:45.248][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-01-14 12:35:45.278][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:45.280][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:45.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.282][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:45.284][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:45.285][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:45.286][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.287][ef$get] fields variable is a list.
biodb.INFO [2025-01-14 12:35:45.292][biodb::testThat]
biodb.INFO [2025-01-14 12:35:45.293][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-01-14 12:35:45.294][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:35:45.295][biodb::testThat]
biodb.TRACE[2025-01-14 12:35:45.323][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:45.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:45.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:45.327][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:45.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:45.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:45.332][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:45.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:45.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:45.400][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:35:45.404][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:35:45.406][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-14 12:35:45.407][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:35:45.408][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-01-14 12:35:45.427][biodb::testThat]
biodb.INFO [2025-01-14 12:35:45.428][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-01-14 12:35:45.429][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:35:45.430][biodb::testThat]
biodb.TRACE[2025-01-14 12:35:45.452][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:45.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:45.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:45.456][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:45.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:45.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:45.460][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:45.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:45.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:45.464][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:45.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:45.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:45.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:45.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:45.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:45.471][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:45.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:45.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:45.474][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-14 12:35:45.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-14 12:35:45.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:45.478][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-14 12:35:45.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-14 12:35:45.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:45.481][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-14 12:35:45.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-14 12:35:45.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:45.485][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-14 12:35:45.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-14 12:35:45.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:45.506][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:45.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:45.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:45.510][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:45.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:45.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:45.513][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:45.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:45.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:45.524][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:45.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:45.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:45.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:45.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:45.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:45.530][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:45.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:45.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:45.534][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-14 12:35:45.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-14 12:35:45.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:45.537][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-14 12:35:45.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-14 12:35:45.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:45.540][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-14 12:35:45.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-14 12:35:45.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:45.544][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-14 12:35:45.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-14 12:35:45.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:45.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-14 12:35:45.554][biodb::testThat]
biodb.INFO [2025-01-14 12:35:45.555][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-01-14 12:35:45.556][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:35:45.556][biodb::testThat]
biodb.INFO [2025-01-14 12:35:45.564][biodb::testThat]
biodb.INFO [2025-01-14 12:35:45.565][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-01-14 12:35:45.566][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:35:45.567][biodb::testThat]
biodb.INFO [2025-01-14 12:35:45.575][biodb::testThat]
biodb.INFO [2025-01-14 12:35:45.576][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-01-14 12:35:45.577][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:35:45.577][biodb::testThat]
biodb.DEBUG[2025-01-14 12:35:45.581][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-01-14 12:35:46.186][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-01-14 12:35:46.830][biodb::testThat]
biodb.INFO [2025-01-14 12:35:46.831][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-01-14 12:35:46.832][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:35:46.833][biodb::testThat]
biodb.DEBUG[2025-01-14 12:35:46.994][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[2025-01-14 12:35:47.158][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:47.160][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:47.161][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.162][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.163][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:47.163][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:47.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.165][ef$get] fields variable is a list.
biodb.INFO [2025-01-14 12:35:47.168][biodb::testThat]
biodb.INFO [2025-01-14 12:35:47.168][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-01-14 12:35:47.169][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:35:47.170][biodb::testThat]
biodb.TRACE[2025-01-14 12:35:47.181][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:47.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:47.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.185][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:47.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:47.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.188][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:47.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:47.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:47.287][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:35:47.291][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:35:47.293][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-14 12:35:47.294][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:35:47.296][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-01-14 12:35:47.375][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:35:47.379][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:35:47.380][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-14 12:35:47.381][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:35:47.383][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-01-14 12:35:47.398][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-14 12:35:47.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-14 12:35:47.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.406][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:47.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:47.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.410][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:47.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:47.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.413][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:47.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:47.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.417][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:47.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:47.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.420][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:47.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:47.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:47.432][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:35:47.449][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:47.451][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:47.474][private$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[2025-01-14 12:35:47.554][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[2025-01-14 12:35:47.632][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:47.634][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-01-14 12:35:47.638][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-01-14 12:35:47.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:47.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:47.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:47.648][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:47.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:47.650][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:47.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:47.652][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-01-14 12:35:47.696][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:47.698][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-01-14 12:35:47.699][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:47.700][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:47.701][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:47.702][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:47.703][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:47.710][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:47.716][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:47.717][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:47.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:47.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:47.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:47.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:47.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:47.728][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-01-14 12:35:47.731][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:47.732][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:47.733][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-01-14 12:35:47.811][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-01-14 12:35:47.892][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:47.895][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-01-14 12:35:47.898][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-01-14 12:35:47.901][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-01-14 12:35:47.902][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:47.903][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:47.905][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:47.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:47.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:47.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:47.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:47.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:47.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:47.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:47.918][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:47.919][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:47.919][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.920][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:47.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:47.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.926][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:47.927][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:47.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.929][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.930][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:47.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:47.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.933][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:47.934][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:47.935][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.936][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.938][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:47.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:47.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.941][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:47.942][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:47.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.944][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.945][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:47.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:47.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.948][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:47.950][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:47.950][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.951][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.953][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:47.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:47.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.957][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:47.958][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:47.959][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.960][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.961][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:47.962][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:47.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.964][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.965][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:47.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:47.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.969][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:47.969][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:47.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.971][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.972][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:47.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:47.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.976][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:47.977][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:47.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.989][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.991][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:47.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:47.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:47.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:47.995][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:47.996][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:47.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.000][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.002][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:48.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:48.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.007][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:48.009][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:48.010][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.012][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.013][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:48.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:48.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:48.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:48.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:48.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:48.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:48.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:48.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:48.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:48.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:48.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:48.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:48.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:48.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:48.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:48.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:48.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:48.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:48.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:48.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:48.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:48.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:48.057][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-01-14 12:35:48.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:48.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:48.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:48.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:48.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:48.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:48.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:48.079][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[2025-01-14 12:35:48.083][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:48.084][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:48.086][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-01-14 12:35:48.168][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-01-14 12:35:48.247][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:48.250][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-01-14 12:35:48.254][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-01-14 12:35:48.280][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:48.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:48.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:48.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:48.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:48.290][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:48.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:48.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:48.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:48.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.295][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:48.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:48.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:48.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:48.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:48.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:48.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:48.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:48.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:48.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:48.312][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:48.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:48.314][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-01-14 12:35:48.315][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:48.317][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-01-14 12:35:48.319][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:48.320][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:48.321][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:48.322][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:48.323][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:48.324][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:48.339][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:48.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:48.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:48.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:48.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:48.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:48.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:48.351][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-01-14 12:35:48.354][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:48.355][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-01-14 12:35:48.356][rule$waitAsNeeded] Wait 0.117445 second(s).
biodb.TRACE[2025-01-14 12:35:48.625][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-01-14 12:35:48.701][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-01-14 12:35:48.785][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:48.787][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-01-14 12:35:48.790][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-01-14 12:35:48.793][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-01-14 12:35:48.795][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:48.796][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:48.797][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:48.798][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:48.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:48.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:48.815][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:48.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:48.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:48.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:48.821][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:48.822][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:48.823][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.824][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:48.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:48.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.829][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:48.830][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:48.831][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.832][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.833][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:48.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:48.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.837][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:48.838][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:48.839][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.840][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.842][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:48.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:48.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.845][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:48.847][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:48.848][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.849][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.850][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:48.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:48.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.855][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:48.856][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:48.856][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.857][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.858][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:48.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:48.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.862][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:48.863][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:48.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.865][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.866][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:48.867][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:48.868][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.869][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.871][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:48.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:48.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.875][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:48.876][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:48.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.878][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:48.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:48.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.883][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:48.883][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:48.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.885][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.886][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:48.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:48.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.890][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:48.891][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:48.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.892][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.893][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:48.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:48.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.897][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:48.898][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:48.898][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.899][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.900][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:48.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:48.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:48.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:48.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:48.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:48.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:48.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:48.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:48.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:48.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:48.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:48.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:48.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:48.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:48.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:48.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:48.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:48.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:48.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:48.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:48.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:48.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:48.945][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-01-14 12:35:48.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:48.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:48.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.951][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:48.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:48.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:48.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:48.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:48.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:48.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:48.978][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[2025-01-14 12:35:48.982][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:35:48.983][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-14 12:35:48.985][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:35:48.986][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-01-14 12:35:48.990][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:48.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:48.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:48.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:48.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:49.000][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:49.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:49.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.005][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.008][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:49.012][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:49.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:49.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:49.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:49.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:49.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:49.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:49.022][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-01-14 12:35:49.023][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:49.024][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-01-14 12:35:49.026][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:49.027][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:49.028][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:49.028][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:49.029][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:49.030][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:49.033][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:49.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:49.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:49.047][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:49.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:49.049][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:49.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:49.051][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-01-14 12:35:49.053][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:49.054][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:49.056][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-01-14 12:35:49.146][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-01-14 12:35:49.225][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:49.228][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-01-14 12:35:49.232][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-01-14 12:35:49.234][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-01-14 12:35:49.236][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:49.237][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:49.238][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:49.240][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:49.241][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:49.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:49.247][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:49.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:49.249][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:49.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:49.252][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:49.254][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:49.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.256][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:49.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:49.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.260][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:49.261][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:49.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.263][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.264][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:49.265][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:49.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.267][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.268][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:49.269][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:49.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.271][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.272][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:49.273][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:49.273][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.274][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.275][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:49.276][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:49.277][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.278][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.279][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:49.280][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.281][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.282][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:49.283][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:49.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.285][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.286][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:49.287][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:49.288][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.288][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.290][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:49.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:49.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.293][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:49.294][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:49.295][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.296][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.297][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:49.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:49.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.301][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:49.301][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:49.302][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.303][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:49.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:49.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:49.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:49.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:49.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:49.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:49.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:49.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:49.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:49.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:49.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:49.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:49.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:49.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:49.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:49.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:49.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:49.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:49.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:49.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:49.351][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-01-14 12:35:49.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:49.371][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:49.372][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:49.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:49.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:49.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:49.380][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:49.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:49.382][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-01-14 12:35:49.383][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:49.384][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-01-14 12:35:49.385][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:49.386][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:49.387][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:49.388][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:49.389][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:49.390][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:49.393][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:49.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:49.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:49.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:49.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:49.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:49.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:49.404][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-01-14 12:35:49.407][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:49.408][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:49.410][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-01-14 12:35:49.495][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-01-14 12:35:49.578][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:49.580][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-01-14 12:35:49.584][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-01-14 12:35:49.587][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-01-14 12:35:49.588][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:49.590][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:49.591][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:49.592][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:49.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:49.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:49.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:49.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:49.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:49.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:49.614][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:49.615][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:49.615][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.616][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:49.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:49.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.621][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:49.622][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:49.623][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.624][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.625][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:49.627][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:49.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.628][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.630][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:49.630][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:49.631][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.632][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.633][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:49.634][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:49.635][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.636][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.637][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:49.638][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:49.638][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.639][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.640][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:49.641][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.642][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.643][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.644][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:49.645][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:49.646][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.646][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.647][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:49.648][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:49.649][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.650][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.651][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:49.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:49.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.655][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:49.656][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:49.657][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.657][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.659][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:49.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:49.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.662][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:49.663][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:49.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.664][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:49.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:49.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:49.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:49.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:49.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:49.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:49.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:49.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:49.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:49.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:49.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:49.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:49.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:49.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:49.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:49.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:49.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:49.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:49.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:49.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:49.737][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-01-14 12:35:49.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.743][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:49.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:49.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:49.757][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:49.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:49.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:49.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:49.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:49.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:49.768][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-01-14 12:35:49.769][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:49.771][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-01-14 12:35:49.772][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:49.773][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:49.774][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:49.775][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:49.776][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:49.777][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:49.780][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:49.781][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:49.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:49.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:49.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:49.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:49.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:49.791][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-01-14 12:35:49.794][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:49.795][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:49.796][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-01-14 12:35:49.881][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-01-14 12:35:49.967][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:49.970][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-01-14 12:35:49.974][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-01-14 12:35:49.977][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-01-14 12:35:49.979][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:49.980][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:49.981][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:49.983][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:49.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:49.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:49.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:49.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:49.992][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:49.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:49.996][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:49.997][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:49.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:49.998][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:49.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.004][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:50.005][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:50.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.007][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.008][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:50.010][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:50.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.012][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.013][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:50.015][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:50.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.017][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.018][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:50.019][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:50.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.021][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.022][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:50.032][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:50.034][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.035][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.037][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:50.038][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.040][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.041][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:50.042][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:50.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.043][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.044][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:50.045][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:50.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.047][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.048][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:50.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:50.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.052][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:50.053][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:50.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.054][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.055][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:50.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:50.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.059][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:50.060][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:50.061][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.062][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.063][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:50.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:50.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:50.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:50.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:50.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:50.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:50.096][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-01-14 12:35:50.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.111][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:50.114][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:50.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:50.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:50.122][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:50.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:50.123][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:50.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:50.125][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-01-14 12:35:50.126][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:50.128][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-01-14 12:35:50.129][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:50.130][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:50.137][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:50.139][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:50.140][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:50.141][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:50.144][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:50.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:50.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:50.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:50.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:50.154][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:50.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:50.156][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-01-14 12:35:50.159][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:50.160][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:50.161][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-01-14 12:35:50.247][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-01-14 12:35:50.331][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:50.333][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-01-14 12:35:50.337][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-01-14 12:35:50.340][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-01-14 12:35:50.342][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:50.343][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:50.344][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:50.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:50.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:50.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:50.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:50.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:50.354][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:50.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:50.358][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.359][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.360][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.365][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:50.366][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:50.367][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.367][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.368][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:50.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:50.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.372][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:50.373][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:50.374][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.374][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.376][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:50.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:50.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.379][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:50.380][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:50.381][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.381][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.382][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:50.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:50.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.386][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:50.387][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:50.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.388][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.389][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:50.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:50.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.393][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:50.394][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:50.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.395][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.396][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:50.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:50.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.399][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:50.401][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.403][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.404][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:50.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.407][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:50.408][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:50.409][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.410][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:50.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:50.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.425][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:50.426][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:50.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.427][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.429][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:50.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:50.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.432][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:50.433][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:50.434][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.435][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.436][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:50.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:50.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.439][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:50.440][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:50.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.442][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.443][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:50.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:50.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:50.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:50.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:50.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:50.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:50.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:50.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:50.478][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-01-14 12:35:50.479][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.483][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.486][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:50.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:50.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:50.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:50.498][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:50.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:50.500][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:50.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:50.502][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-01-14 12:35:50.503][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:50.504][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-01-14 12:35:50.505][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:50.506][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:50.508][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:50.509][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:50.510][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:50.511][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:50.514][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:50.515][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:50.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:50.528][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:50.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:50.530][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:50.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:50.534][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-01-14 12:35:50.538][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:50.539][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:50.540][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-01-14 12:35:50.622][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-01-14 12:35:50.730][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:50.733][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-01-14 12:35:50.737][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-01-14 12:35:50.739][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-01-14 12:35:50.741][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:50.742][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:50.743][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:50.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:50.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:50.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:50.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:50.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:50.754][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:50.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:50.757][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.758][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.760][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.764][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:50.765][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:50.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.767][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.768][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:50.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:50.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.771][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:50.772][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:50.773][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.774][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.775][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:50.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:50.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.779][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:50.780][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:50.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.782][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.783][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:50.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:50.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.786][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:50.787][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:50.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.788][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.789][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:50.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:50.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.793][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:50.793][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:50.794][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.795][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.796][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:50.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:50.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.799][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:50.800][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.801][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.802][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.803][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:50.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.806][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:50.807][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:50.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.808][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:50.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:50.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.813][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:50.814][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:50.814][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.815][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.816][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:50.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:50.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.831][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:50.832][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:50.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.834][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.835][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:50.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:50.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.839][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:50.839][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:50.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.841][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.842][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:50.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:50.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:50.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:50.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:50.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:50.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.856][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:50.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:50.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:50.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:50.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:50.879][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-01-14 12:35:50.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:50.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:50.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:50.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:50.891][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:50.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:50.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:50.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:50.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:50.900][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:50.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:50.902][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-01-14 12:35:50.903][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:50.905][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-01-14 12:35:50.906][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:50.907][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:50.908][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:50.908][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:50.909][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:50.910][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:50.913][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:50.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:50.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:50.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:50.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:50.922][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:50.923][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[2025-01-14 12:35:50.924][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-01-14 12:35:50.927][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:50.928][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:50.930][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-01-14 12:35:51.023][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-01-14 12:35:51.114][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:51.117][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-01-14 12:35:51.122][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-01-14 12:35:51.125][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-01-14 12:35:51.127][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:51.128][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:51.130][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:51.132][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:51.133][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:51.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:51.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:51.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:51.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:51.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:51.145][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:51.146][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:51.147][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.148][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:51.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:51.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.153][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:51.154][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:51.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.155][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.157][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:51.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:51.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.160][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:51.161][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:51.162][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.163][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.164][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:51.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:51.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.167][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:51.168][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:51.169][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.170][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.171][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:51.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:51.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.174][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:51.175][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:51.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.177][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.178][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:51.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:51.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.182][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:51.183][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:51.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.186][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.187][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:51.188][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:51.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.189][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.191][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:51.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:51.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.194][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:51.196][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:51.197][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.198][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:51.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:51.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.203][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:51.203][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:51.204][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.205][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.206][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:51.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:51.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.210][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:51.211][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:51.211][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.212][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.213][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:51.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:51.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.217][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:51.218][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:51.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.220][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.221][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:51.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:51.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:51.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:51.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:51.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:51.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:51.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:51.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.245][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:51.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:51.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:51.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:51.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:51.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:51.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:51.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:51.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:51.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:51.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:51.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:51.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:51.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:51.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:51.270][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-01-14 12:35:51.271][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:51.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:51.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:51.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:51.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.281][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:51.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:51.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:51.285][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:51.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:51.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:51.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:51.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:51.294][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:51.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:51.296][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-01-14 12:35:51.297][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:51.299][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-01-14 12:35:51.301][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:51.302][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:51.303][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:51.304][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:51.305][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:51.305][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:51.309][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:51.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:51.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:51.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:51.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:51.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:51.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:51.320][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-01-14 12:35:51.323][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:51.324][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:51.326][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-01-14 12:35:51.419][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-01-14 12:35:51.504][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:51.507][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-01-14 12:35:51.510][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-01-14 12:35:51.513][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-01-14 12:35:51.515][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:51.516][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:51.517][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:51.528][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:51.530][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:51.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:51.537][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:51.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:51.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:51.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:51.541][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:51.542][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:51.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.544][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:51.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:51.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.548][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:51.549][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:51.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.551][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.552][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:51.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:51.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.555][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:51.556][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:51.557][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.558][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.559][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:51.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:51.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.562][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:51.563][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:51.564][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.564][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.565][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:51.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:51.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.569][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:51.570][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:51.570][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.571][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.572][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:51.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:51.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.575][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:51.576][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:51.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.578][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.579][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:51.580][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:51.581][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.581][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.582][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:51.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:51.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.586][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:51.586][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:51.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.588][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:51.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:51.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.592][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:51.593][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:51.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.594][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.596][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:51.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:51.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.599][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:51.600][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:51.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.602][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.603][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:51.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:51.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.606][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:51.607][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:51.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.608][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.609][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:51.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:51.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:51.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:51.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:51.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:51.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:51.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:51.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:51.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:51.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:51.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:51.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:51.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:51.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:51.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:51.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:51.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:51.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:51.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:51.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:51.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:51.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:51.654][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-01-14 12:35:51.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:51.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:51.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.658][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:51.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:51.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.662][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:51.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:51.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:51.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:51.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:51.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:51.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:51.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:51.674][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:51.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:51.676][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-01-14 12:35:51.677][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:51.678][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-01-14 12:35:51.679][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:51.680][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:51.681][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:51.682][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:51.683][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:51.684][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:51.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:51.688][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:51.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:51.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:51.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:51.697][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:51.697][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[2025-01-14 12:35:51.699][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-01-14 12:35:51.701][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:51.702][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:51.704][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-01-14 12:35:51.788][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-01-14 12:35:51.874][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:51.877][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-01-14 12:35:51.881][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-01-14 12:35:51.884][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-01-14 12:35:51.885][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:51.886][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:51.887][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:51.889][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:51.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:51.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:51.896][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:51.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:51.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:51.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:51.901][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:51.902][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:51.903][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.914][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:51.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:51.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.922][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:51.923][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:51.924][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.924][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.926][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:51.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:51.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.929][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:51.930][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:51.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.932][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.933][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:51.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:51.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.937][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:51.938][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:51.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.940][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.942][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:51.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:51.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.946][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:51.947][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:51.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.949][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.950][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:51.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:51.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.954][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:51.955][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:51.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.957][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.958][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:51.960][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:51.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.962][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.963][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:51.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:51.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.967][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:51.968][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:51.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.970][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.971][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:51.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:51.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.974][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:51.975][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:51.976][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.977][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.978][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:51.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:51.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.982][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:51.983][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:51.984][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.985][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.986][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:51.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:51.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.990][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:51.991][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:51.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.992][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.993][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:51.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:51.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:51.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:51.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:51.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:51.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:52.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:52.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:52.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:52.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:52.039][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-01-14 12:35:52.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:52.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:52.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.043][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:52.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:52.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.047][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:52.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:52.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:52.050][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:52.051][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:52.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:52.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:52.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:52.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:52.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:52.062][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-01-14 12:35:52.063][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:52.064][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-01-14 12:35:52.065][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:52.066][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:52.067][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:52.068][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:52.069][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:52.070][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:52.073][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:52.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:52.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:52.081][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:52.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:52.083][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:52.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:52.085][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-01-14 12:35:52.088][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:52.089][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:52.091][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-01-14 12:35:52.175][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-01-14 12:35:52.260][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:52.262][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-01-14 12:35:52.266][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-01-14 12:35:52.268][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-01-14 12:35:52.270][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:52.271][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:52.272][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:52.274][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:52.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:52.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:52.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:52.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:52.282][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:52.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:52.285][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.286][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.288][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.293][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:52.293][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:52.294][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.295][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.296][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:52.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:52.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.311][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:52.312][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:52.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.314][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.316][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:52.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:52.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.319][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:52.320][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:52.321][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.322][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.323][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:52.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:52.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.326][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:52.327][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:52.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.329][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.330][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:52.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:52.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.333][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:52.334][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:52.335][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.336][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.337][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:52.338][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:52.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.340][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.341][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:52.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:52.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.344][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:52.345][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:52.346][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.347][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:52.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:52.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.351][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:52.352][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:52.353][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.354][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.355][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:52.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:52.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.358][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:52.359][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:52.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.361][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.362][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:52.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:52.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.365][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:52.366][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:52.367][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.367][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.368][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:52.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:52.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:52.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:52.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:52.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:52.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:52.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:52.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:52.414][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-01-14 12:35:52.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:52.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:52.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.418][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:52.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:52.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:52.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:52.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:52.424][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:52.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:52.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:52.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:52.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:52.433][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:52.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:52.435][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-01-14 12:35:52.436][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:52.437][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-01-14 12:35:52.439][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:52.440][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:52.440][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:52.441][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:52.442][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:52.443][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:52.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:52.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:52.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:52.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:52.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:52.455][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:52.455][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[2025-01-14 12:35:52.456][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-01-14 12:35:52.459][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:52.460][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:52.461][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-01-14 12:35:52.546][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-01-14 12:35:52.635][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:52.637][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-01-14 12:35:52.641][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-01-14 12:35:52.643][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-01-14 12:35:52.645][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:52.646][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:52.647][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:52.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:52.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:52.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:52.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:52.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:52.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:52.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:52.662][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.663][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.664][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.669][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:52.669][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:52.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.671][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.672][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:52.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:52.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.675][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:52.676][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:52.677][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.678][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.679][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:52.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:52.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.682][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:52.683][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:52.684][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.684][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.695][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:52.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:52.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.700][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:52.701][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:52.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.702][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.703][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:52.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:52.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.707][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:52.708][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:52.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.709][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.710][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:52.711][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:52.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.713][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.714][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:52.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:52.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.717][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:52.718][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:52.719][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.720][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.721][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:52.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:52.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.724][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:52.725][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:52.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.727][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.728][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:52.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:52.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.731][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:52.732][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:52.733][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.733][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.734][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:52.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:52.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.738][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:52.739][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:52.739][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.740][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.741][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:52.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:52.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.744][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:52.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:52.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:52.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:52.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.754][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:52.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:52.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:52.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:52.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:52.776][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-01-14 12:35:52.777][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:52.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:52.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:52.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:52.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:52.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:52.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:52.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:52.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:52.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:52.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:52.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:52.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:52.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:52.804][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:52.804][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[2025-01-14 12:35:52.805][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-01-14 12:35:52.806][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:52.808][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-01-14 12:35:52.809][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:52.810][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:52.811][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:52.812][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:52.812][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:52.813][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:52.816][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:52.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:52.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:52.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:52.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:52.825][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:52.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:52.827][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-01-14 12:35:52.830][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:52.831][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:52.832][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-01-14 12:35:52.916][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-01-14 12:35:52.998][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:53.001][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-01-14 12:35:53.005][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-01-14 12:35:53.008][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-01-14 12:35:53.010][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:53.011][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:53.012][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:53.013][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:53.014][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:53.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:53.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:53.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:53.022][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:53.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:53.025][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.026][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.028][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.032][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:53.033][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:53.034][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.035][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.036][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:53.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:53.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.039][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:53.040][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:53.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.042][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.043][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:53.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:53.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.046][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:53.047][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:53.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.048][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.050][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:53.051][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:53.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.052][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.053][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:53.054][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:53.055][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.055][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.056][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:53.057][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.058][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.069][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.070][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:53.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.074][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:53.075][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:53.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.077][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:53.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:53.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.081][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:53.082][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:53.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.083][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.085][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:53.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:53.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.088][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:53.089][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:53.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.090][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.091][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:53.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:53.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.095][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:53.096][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:53.097][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.097][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:53.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:53.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:53.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:53.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:53.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:53.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:53.130][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-01-14 12:35:53.131][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.135][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.138][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:53.141][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:53.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:53.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:53.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:53.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:53.150][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:53.151][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[2025-01-14 12:35:53.152][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-01-14 12:35:53.153][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:53.155][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-01-14 12:35:53.156][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:53.157][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:53.158][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:53.159][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:53.160][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:53.161][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:53.172][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:53.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:53.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:53.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:53.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:53.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:53.182][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[2025-01-14 12:35:53.183][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-01-14 12:35:53.186][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:53.187][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:53.189][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-01-14 12:35:53.271][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-01-14 12:35:53.361][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:53.363][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-01-14 12:35:53.368][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-01-14 12:35:53.371][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-01-14 12:35:53.372][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:53.373][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:53.375][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:53.376][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:53.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:53.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:53.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:53.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:53.385][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:53.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:53.388][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.389][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.391][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.396][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:53.397][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:53.398][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.399][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.400][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:53.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:53.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.404][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:53.405][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:53.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.406][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.407][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:53.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:53.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.411][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:53.411][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:53.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.413][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.414][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:53.415][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:53.416][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.416][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.417][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:53.418][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:53.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.420][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.421][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:53.422][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.423][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.424][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:53.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.428][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:53.428][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:53.429][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.430][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:53.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:53.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.435][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:53.436][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:53.437][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.438][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.439][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:53.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:53.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.443][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:53.450][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:53.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.456][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.457][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:53.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:53.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.461][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:53.462][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:53.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.463][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:53.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:53.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:53.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:53.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:53.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:53.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:53.498][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-01-14 12:35:53.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.502][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:53.509][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:53.509][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:53.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:53.516][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:53.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:53.518][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:53.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:53.519][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-01-14 12:35:53.520][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:53.522][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-01-14 12:35:53.523][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:53.524][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:53.525][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:53.526][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:53.527][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:53.527][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:53.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:53.532][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:53.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:53.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:53.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:53.541][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:53.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:53.542][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-01-14 12:35:53.545][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:53.546][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:53.548][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-01-14 12:35:53.632][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-01-14 12:35:53.717][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:53.726][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-01-14 12:35:53.736][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-01-14 12:35:53.739][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-01-14 12:35:53.742][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:53.743][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:53.745][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:53.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:53.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:53.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:53.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:53.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:53.756][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:53.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:53.759][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.760][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.762][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.767][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:53.768][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:53.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.770][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.771][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:53.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:53.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.775][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:53.776][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:53.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.778][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.779][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:53.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:53.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.783][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:53.784][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:53.785][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.786][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.788][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:53.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:53.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.791][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:53.792][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:53.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.794][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.795][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:53.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:53.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.798][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:53.799][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:53.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.801][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.802][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:53.803][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.804][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.804][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.805][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:53.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.809][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:53.810][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:53.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.811][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:53.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:53.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.815][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:53.816][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:53.817][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.818][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.819][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:53.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:53.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.822][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:53.823][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:53.824][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.825][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.826][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:53.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:53.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.829][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:53.830][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:53.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.831][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.832][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:53.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:53.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:53.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:53.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:53.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:53.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:53.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:53.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:53.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:53.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:53.876][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-01-14 12:35:53.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:53.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:53.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:53.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:53.886][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:53.887][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:53.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:53.892][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:53.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:53.894][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:53.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:53.896][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-01-14 12:35:53.897][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:53.898][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-01-14 12:35:53.899][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:53.900][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:53.901][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:53.902][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:53.903][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:53.904][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:53.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:53.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:53.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:53.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:53.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:53.915][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:53.916][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[2025-01-14 12:35:53.917][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-01-14 12:35:53.920][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:53.921][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:53.923][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-01-14 12:35:54.025][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-01-14 12:35:54.118][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:54.121][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-01-14 12:35:54.125][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-01-14 12:35:54.127][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-01-14 12:35:54.129][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:54.130][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:54.131][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:54.147][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:54.149][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:54.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:54.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:54.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:54.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:54.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:54.162][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.163][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.164][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.169][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:54.170][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:54.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.172][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.173][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:54.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:54.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.177][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:54.178][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:54.179][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.179][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.181][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:54.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:54.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.184][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:54.185][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:54.186][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.186][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.187][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:54.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:54.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.191][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:54.192][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:54.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.193][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.194][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:54.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:54.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.198][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:54.198][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:54.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.200][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.201][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:54.202][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:54.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.204][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.205][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:54.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:54.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.208][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:54.209][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:54.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.211][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.212][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:54.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:54.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.216][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:54.216][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:54.217][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.218][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.219][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:54.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:54.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.222][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:54.223][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:54.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.225][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.226][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:54.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:54.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.229][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:54.230][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:54.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.231][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.232][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:54.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:54.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:54.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:54.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:54.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:54.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.252][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:54.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:54.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:54.277][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-01-14 12:35:54.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:54.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:54.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.282][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:54.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:54.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:54.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:54.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:54.288][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:54.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:54.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:54.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:54.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:54.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:54.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:54.299][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-01-14 12:35:54.300][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:54.302][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-01-14 12:35:54.303][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:54.304][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:54.305][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:54.306][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:54.307][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:54.308][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:54.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:54.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:54.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:54.318][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:54.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:54.320][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:54.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:54.322][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-01-14 12:35:54.325][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:54.326][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:54.328][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-01-14 12:35:54.410][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-01-14 12:35:54.497][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:54.500][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-01-14 12:35:54.504][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-01-14 12:35:54.506][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-01-14 12:35:54.508][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:54.509][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:54.510][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:54.511][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:54.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:54.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:54.518][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:54.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:54.520][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:54.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:54.524][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.525][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.537][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.543][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:54.544][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:54.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.545][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.546][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:54.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:54.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.550][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:54.550][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:54.551][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.552][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.553][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:54.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:54.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.556][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:54.557][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:54.558][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.559][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.560][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:54.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:54.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.563][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:54.564][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:54.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.565][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.567][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:54.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:54.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.570][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:54.571][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:54.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.572][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.573][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:54.574][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:54.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.575][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.576][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:54.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:54.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.580][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:54.581][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:54.581][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.582][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:54.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:54.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.586][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:54.587][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:54.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.589][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.590][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:54.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:54.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.593][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:54.594][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:54.595][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.595][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.596][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:54.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:54.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.599][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:54.600][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:54.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.602][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.603][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:54.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:54.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:54.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:54.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:54.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:54.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:54.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:54.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:54.646][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-01-14 12:35:54.647][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:54.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:54.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.650][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:54.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:54.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.654][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:54.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:54.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:54.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:54.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:54.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:54.664][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:54.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:54.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:54.666][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[2025-01-14 12:35:54.667][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-01-14 12:35:54.668][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:54.670][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-01-14 12:35:54.671][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:54.672][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:54.673][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:54.673][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:54.674][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:54.675][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:54.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:54.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:54.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:54.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:54.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:54.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:54.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:54.688][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-01-14 12:35:54.691][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:54.692][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:54.693][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-01-14 12:35:54.773][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-01-14 12:35:54.852][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:54.855][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-01-14 12:35:54.858][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-01-14 12:35:54.861][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-01-14 12:35:54.863][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:54.864][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:54.865][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:54.867][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:54.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:54.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:54.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:54.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:54.876][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:54.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:54.879][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.880][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.881][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.886][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:54.887][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:54.888][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.888][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.890][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:54.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:54.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.903][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:54.905][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:54.906][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.907][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.908][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:54.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:54.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.912][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:54.913][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:54.913][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.914][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.915][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:54.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:54.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.919][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:54.919][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:54.920][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.921][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.922][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:54.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:54.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.925][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:54.926][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:54.927][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.928][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.929][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:54.930][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:54.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.931][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.932][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:54.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:54.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.936][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:54.937][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:54.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.938][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.939][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:54.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:54.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.942][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:54.943][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:54.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.945][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.946][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:54.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:54.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.949][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:54.950][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:54.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.951][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.952][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:54.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:54.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.956][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:54.957][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:54.957][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.958][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.959][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:54.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:54.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:54.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:54.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:54.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:54.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:54.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:54.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:54.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:54.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:54.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:54.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:55.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:55.002][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-01-14 12:35:55.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:55.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:55.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.006][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:55.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:55.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.009][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:55.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:55.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:55.012][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:55.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:55.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:55.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:55.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:55.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:55.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:55.023][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-01-14 12:35:55.024][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:55.025][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-01-14 12:35:55.027][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:55.028][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:55.029][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:55.029][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:55.030][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:55.031][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:55.034][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:55.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:55.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:55.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:55.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:55.044][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:55.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:55.046][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-01-14 12:35:55.049][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:55.050][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:55.051][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-01-14 12:35:55.143][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-01-14 12:35:55.226][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:55.229][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-01-14 12:35:55.233][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-01-14 12:35:55.236][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-01-14 12:35:55.237][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:55.239][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:55.240][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:55.241][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:55.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:55.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:55.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:55.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:55.250][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:55.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:55.253][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:55.254][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:55.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.256][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:55.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:55.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.261][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:55.261][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:55.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.263][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.264][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:55.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:55.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.267][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:55.268][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:55.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.270][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.271][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:55.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:55.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.275][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:55.276][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:55.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.287][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.289][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:55.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:55.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.295][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:55.296][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:55.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.297][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.299][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:55.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:55.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.302][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:55.303][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:55.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.305][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.307][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:55.308][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:55.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.309][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.310][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:55.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:55.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.314][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:55.315][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:55.316][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.317][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:55.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:55.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.321][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:55.322][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:55.324][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.325][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.326][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:55.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:55.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.329][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:55.330][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:55.331][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.332][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.333][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:55.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:55.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.337][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:55.337][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:55.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.339][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.340][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:55.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:55.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:55.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:55.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.347][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:55.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:55.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:55.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:55.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.354][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:55.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:55.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:55.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:55.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:55.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:55.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:55.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:55.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:55.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:55.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:55.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:55.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:55.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:55.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:55.382][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-01-14 12:35:55.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:55.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:55.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:55.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:55.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.400][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:55.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:55.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:55.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:55.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:55.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:55.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:55.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:55.416][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:55.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:55.418][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-01-14 12:35:55.419][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:55.420][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-01-14 12:35:55.422][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:55.424][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:55.425][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:55.426][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:55.427][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:55.428][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:55.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:55.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:55.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:55.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:55.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:55.441][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:55.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:55.444][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-01-14 12:35:55.447][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:55.448][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:55.449][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-01-14 12:35:55.528][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-01-14 12:35:55.613][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:55.616][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-01-14 12:35:55.620][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-01-14 12:35:55.624][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-01-14 12:35:55.625][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:55.626][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:55.627][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:55.629][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:55.630][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:55.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:55.636][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:55.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:55.638][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:55.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:55.641][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:55.642][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:55.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.643][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:55.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:55.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.648][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:55.649][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:55.649][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.650][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.651][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:55.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:55.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.655][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:55.655][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:55.656][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.657][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.658][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:55.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:55.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.662][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:55.663][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:55.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.664][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.665][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:55.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:55.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.668][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:55.669][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:55.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.671][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.672][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:55.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:55.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.686][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:55.687][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:55.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.689][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.691][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:55.692][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:55.692][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.693][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.694][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:55.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:55.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.698][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:55.699][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:55.699][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.700][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.701][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:55.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:55.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.705][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:55.705][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:55.706][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.707][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.708][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:55.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:55.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.712][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:55.713][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:55.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.714][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.716][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:55.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:55.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.721][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:55.723][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:55.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.725][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.726][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:55.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:55.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.730][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:55.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:55.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:55.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:55.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:55.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:55.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:55.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:55.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:55.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:55.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:55.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:55.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:55.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:55.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:55.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:55.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:55.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:55.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:55.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:55.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:55.763][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-01-14 12:35:55.764][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:55.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:55.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:55.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:55.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:55.771][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:55.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:55.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:55.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:55.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:55.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:55.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:55.788][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:55.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:55.790][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:55.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:55.793][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-01-14 12:35:55.794][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:55.796][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-01-14 12:35:55.797][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:55.798][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:55.799][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:55.800][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:55.800][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:55.801][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:55.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:55.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:55.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:55.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:55.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:55.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:55.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:55.814][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-01-14 12:35:55.817][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:55.818][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:55.820][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-01-14 12:35:55.905][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-01-14 12:35:55.988][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:55.991][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-01-14 12:35:55.994][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-01-14 12:35:55.997][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-01-14 12:35:55.999][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:56.001][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:56.002][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:56.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:56.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:56.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:56.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:56.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:56.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:56.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:56.016][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:56.017][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:56.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.019][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:56.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:56.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.023][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:56.024][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:56.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.026][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.027][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:56.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:56.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.030][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:56.031][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:56.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.033][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.034][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:56.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:56.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.038][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:56.038][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:56.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.040][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.041][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:56.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:56.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.044][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:56.045][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:56.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.047][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.048][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:56.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:56.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.051][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:56.052][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:56.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.054][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.055][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:56.056][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.057][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.058][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:56.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.073][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:56.075][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:56.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.076][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:56.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:56.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.081][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:56.082][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:56.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.084][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.085][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:56.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:56.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.088][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:56.089][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:56.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.091][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.092][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:56.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:56.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.096][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:56.096][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:56.097][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.099][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.100][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:56.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:56.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.104][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:56.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:56.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:56.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:56.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:56.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:56.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:56.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:56.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:56.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:56.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:56.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:56.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:56.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:56.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:56.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:56.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:56.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:56.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:56.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:56.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:56.140][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-01-14 12:35:56.141][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.144][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:56.173][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[2025-01-14 12:35:56.185][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:35:56.187][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-14 12:35:56.188][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:35:56.190][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-01-14 12:35:56.194][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:56.195][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:56.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:56.201][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:56.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:56.203][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:56.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:56.205][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:56.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:56.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:56.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:56.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:56.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:56.226][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:56.227][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[2025-01-14 12:35:56.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.231][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.238][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:56.245][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:56.246][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:56.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:56.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:56.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:56.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:56.255][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.TRACE[2025-01-14 12:35:56.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.267][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.271][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:56.275][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:56.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:56.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:56.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:56.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:56.284][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:56.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:56.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.306][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.309][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:56.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:56.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:56.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:56.320][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:56.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:56.322][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:56.323][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.TRACE[2025-01-14 12:35:56.324][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.331][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:56.335][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:56.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:56.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:56.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:56.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:56.344][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:56.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:56.345][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.349][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:56.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:56.357][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:56.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:56.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:56.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:56.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:56.366][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.TRACE[2025-01-14 12:35:56.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:56.378][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:56.379][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:56.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:56.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:56.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:56.387][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:56.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:56.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:56.398][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:56.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:56.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:56.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:56.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:56.416][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:56.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:56.418][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.425][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:56.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:56.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:56.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:56.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:56.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:56.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:56.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:56.439][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.446][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:56.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:56.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:56.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:56.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:56.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:56.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:56.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:56.460][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.463][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.466][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:56.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:56.470][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:56.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:56.476][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:56.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:56.478][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:56.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:56.480][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.483][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.486][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:56.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:56.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:56.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:56.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:56.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:56.499][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:56.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:56.501][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.504][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.508][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:56.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:56.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:56.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:56.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:56.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:56.527][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:56.528][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.TRACE[2025-01-14 12:35:56.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:56.539][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:56.540][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:56.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:56.546][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:56.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:56.548][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:56.548][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[2025-01-14 12:35:56.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.556][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:56.559][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:56.560][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:56.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:56.566][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:56.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:56.568][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:56.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:56.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.576][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:56.579][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:56.580][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:56.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:56.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:56.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:56.587][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:56.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:56.589][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.593][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.596][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:56.599][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:56.600][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:56.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:56.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:56.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:56.608][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:56.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:56.610][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.613][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.624][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:56.629][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:56.630][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:56.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:56.637][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:56.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:56.638][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:56.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:56.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.647][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:56.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:56.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:56.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:56.657][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:56.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:56.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:56.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:56.661][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.664][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.668][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:56.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:56.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:56.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:56.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:56.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:56.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:56.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.695][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:56.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:56.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:56.698][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:56.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:56.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:56.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:56.736][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:35:56.739][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:56.740][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:56.742][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-01-14 12:35:56.829][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-01-14 12:35:56.919][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:56.922][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-01-14 12:35:56.927][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-01-14 12:35:56.931][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:35:56.935][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:56.936][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:56.938][private$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[2025-01-14 12:35:57.023][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[2025-01-14 12:35:57.108][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:57.110][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-01-14 12:35:57.114][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-01-14 12:35:57.118][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:57.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:57.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:57.125][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:57.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:57.127][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:57.128][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[2025-01-14 12:35:57.129][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-01-14 12:35:57.130][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:57.131][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-01-14 12:35:57.133][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:57.134][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:57.135][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:57.135][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:57.136][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:57.137][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:57.140][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:57.141][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:57.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:57.147][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:57.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:57.149][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:57.150][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.DEBUG[2025-01-14 12:35:57.151][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-01-14 12:35:57.154][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:57.155][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:57.156][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-01-14 12:35:57.249][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-01-14 12:35:57.337][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:57.340][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-01-14 12:35:57.344][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-01-14 12:35:57.347][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-01-14 12:35:57.350][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:57.352][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:57.353][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:57.355][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:57.355][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:57.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:57.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:57.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:57.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:57.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:57.384][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:57.386][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:57.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.389][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:57.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:57.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.394][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:57.395][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:57.396][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.397][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.398][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:57.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:57.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.402][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:57.403][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:57.403][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.404][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.406][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:57.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:57.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.409][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:57.410][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:57.411][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.412][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.413][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:57.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:57.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.417][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:57.418][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:57.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.419][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.421][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:57.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:57.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.424][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:57.425][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:57.426][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.426][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.428][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:57.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:57.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.431][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:57.432][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:57.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.434][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.436][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:57.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:57.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.439][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:57.440][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:57.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.442][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.443][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:57.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:57.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.447][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:57.447][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:57.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.449][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.450][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:57.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:57.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.455][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:57.456][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:57.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.458][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.459][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:57.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:57.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.462][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:57.464][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:57.465][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.466][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.467][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:57.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:57.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.471][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:57.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:57.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:57.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:57.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:57.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:57.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:57.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:57.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:57.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:57.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:57.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:57.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:57.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:57.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:57.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:57.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:57.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:57.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:57.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:57.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:57.513][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-01-14 12:35:57.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:57.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:57.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:57.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:57.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.521][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:57.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:57.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:57.524][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:57.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:57.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:57.531][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:57.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:57.533][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:57.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:57.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:57.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:57.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:57.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:57.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:57.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:57.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:57.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:57.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:57.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:57.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:57.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:57.551][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:57.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:57.553][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:57.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:57.555][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-01-14 12:35:57.556][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:35:57.557][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-01-14 12:35:57.558][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:35:57.559][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:35:57.560][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:35:57.561][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:35:57.562][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:35:57.563][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:35:57.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:57.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:57.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:57.573][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:57.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:57.575][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:57.576][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[2025-01-14 12:35:57.577][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-01-14 12:35:57.580][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:57.581][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-01-14 12:35:57.582][rule$waitAsNeeded] Wait 0.159678 second(s).
biodb.TRACE[2025-01-14 12:35:57.893][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-01-14 12:35:57.973][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-01-14 12:35:58.062][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:58.064][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-01-14 12:35:58.079][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-01-14 12:35:58.083][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-01-14 12:35:58.085][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:35:58.086][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:35:58.087][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:35:58.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:58.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:58.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:58.096][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:58.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:58.098][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:58.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:58.101][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:58.102][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:58.103][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.104][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:58.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:58.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.109][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:58.110][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:58.111][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.112][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.113][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:35:58.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:35:58.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.116][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:58.117][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:58.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.119][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.120][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:35:58.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:35:58.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.123][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:58.124][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:58.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.126][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.127][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:35:58.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:35:58.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.131][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:58.131][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:58.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.133][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.134][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:35:58.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:35:58.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.138][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:58.139][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:35:58.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.140][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.142][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:58.142][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:58.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.144][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.145][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:35:58.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:58.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.148][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.149][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.151][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.152][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.155][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:58.156][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:58.157][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.158][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.159][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:35:58.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:35:58.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.162][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:58.163][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:58.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.165][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.166][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:35:58.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:35:58.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.169][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:58.170][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:58.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.172][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.173][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:35:58.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:35:58.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:58.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:58.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:58.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:58.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:58.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:58.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.196][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:58.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:58.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:58.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:58.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:58.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:58.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:58.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:58.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:58.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:58.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:58.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:58.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:35:58.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:35:58.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:58.219][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-01-14 12:35:58.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:58.250][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:35:58.254][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:35:58.255][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-14 12:35:58.257][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:35:58.258][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-01-14 12:35:58.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:58.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:58.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:58.269][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:58.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:58.271][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:58.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:58.273][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:58.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:58.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:58.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:58.512][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:58.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:58.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:58.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:58.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:58.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:58.533][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:58.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:58.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:58.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:58.541][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:58.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:58.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.552][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.555][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:58.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:58.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:58.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:58.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:58.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:58.567][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:58.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:58.568][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.575][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.581][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:58.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:58.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:58.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:58.591][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:58.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:58.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:58.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:58.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.599][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:58.606][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:58.607][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:58.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:58.614][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:58.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:58.616][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:58.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:58.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:58.631][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:58.631][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:58.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:58.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:58.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:58.641][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:58.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:58.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.647][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.651][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:58.656][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:58.656][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:58.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:58.664][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:58.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:58.666][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:58.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:58.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:58.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:58.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:58.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:58.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:58.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:58.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:58.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:58.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:58.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:58.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:58.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:58.712][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:58.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:58.715][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:58.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:58.717][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.721][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:58.730][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:58.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:58.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:58.738][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:58.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:58.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:58.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:58.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:58.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:58.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:58.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:58.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:58.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:58.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:58.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:58.765][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:58.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:58.777][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:58.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:58.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:58.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:58.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:58.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:58.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:58.799][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:58.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:58.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:58.808][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:58.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:58.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:58.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:58.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:58.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:58.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:58.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:58.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:58.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:58.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:58.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:58.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:58.846][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:58.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:58.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:58.854][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:58.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:58.856][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:58.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:58.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:58.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:58.876][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:58.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:58.882][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:58.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:58.884][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:58.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:58.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:58.895][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:58.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:58.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:58.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:58.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:58.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:58.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:58.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:58.915][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:58.916][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:58.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:58.922][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:58.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:58.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:58.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:58.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.929][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.932][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:58.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:58.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:58.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:58.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:58.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:58.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:58.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:58.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.951][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:58.954][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:58.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:58.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:58.977][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:35:58.981][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:35:58.982][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-14 12:35:58.983][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:35:58.985][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-01-14 12:35:58.988][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:58.989][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:58.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:58.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:58.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:58.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:58.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:58.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.006][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.018][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.037][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.052][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.055][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.059][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.065][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.075][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.077][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.080][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.087][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.102][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.104][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.128][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.134][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.138][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.142][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.166][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.173][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.188][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.189][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.207][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.218][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.238][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.239][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.245][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.246][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.248][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.251][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.264][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.266][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.285][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.287][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.309][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.311][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.321][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.322][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.342][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.352][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.354][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.389][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.398][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.400][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.407][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.410][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.411][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.419][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.468][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-01-14 12:35:59.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-01-14 12:35:59.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-14 12:35:59.481][biodb::testThat]
biodb.INFO [2025-01-14 12:35:59.482][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-01-14 12:35:59.483][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:35:59.484][biodb::testThat]
biodb.TRACE[2025-01-14 12:35:59.487][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-14 12:35:59.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-14 12:35:59.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.501][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.508][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.509][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:59.521][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:35:59.525][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:35:59.526][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-01-14 12:35:59.527][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:35:59.529][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-01-14 12:35:59.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.532][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.541][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.546][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.555][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:35:59.558][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:35:59.560][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-01-14 12:35:59.561][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:35:59.571][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-01-14 12:35:59.574][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.575][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.584][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.586][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.589][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.592][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.602][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.604][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.605][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.609][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.612][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:35:59.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.615][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-14 12:35:59.616][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.623][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.625][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.626][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.633][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:35:59.633][private$selectFields]
biodb.TRACE[2025-01-14 12:35:59.634][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-14 12:35:59.635][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-14 12:35:59.636][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:35:59.636][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.637][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.638][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.639][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.639][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.640][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.641][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.642][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.642][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:35:59.643][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:35:59.644][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.645][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.646][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.647][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-14 12:35:59.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.651][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.654][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.666][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-01-14 12:35:59.667][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.668][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.685][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:35:59.685][private$selectFields]
biodb.TRACE[2025-01-14 12:35:59.686][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-14 12:35:59.687][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-14 12:35:59.688][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:35:59.689][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.689][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.692][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.693][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.694][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.695][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.696][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.697][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:35:59.698][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:35:59.699][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.700][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.702][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.703][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-14 12:35:59.704][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.708][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.716][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-14 12:35:59.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:35:59.730][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.737][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:35:59.738][private$selectFields]
biodb.TRACE[2025-01-14 12:35:59.738][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-14 12:35:59.739][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-14 12:35:59.740][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:35:59.741][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.741][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.742][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.743][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.744][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.745][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.745][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:35:59.746][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:35:59.746][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.747][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.748][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.749][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-14 12:35:59.749][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.754][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:35:59.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.758][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-01-14 12:35:59.759][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-14 12:35:59.759][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-14 12:35:59.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:35:59.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:35:59.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:35:59.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:35:59.801][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:35:59.802][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:35:59.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:35:59.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:35:59.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:35:59.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:35:59.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:35:59.811][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:35:59.815][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:35:59.816][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:35:59.818][private$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[2025-01-14 12:35:59.907][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[2025-01-14 12:35:59.982][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:35:59.984][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-01-14 12:35:59.987][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-01-14 12:35:59.991][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[2025-01-14 12:36:00.000][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:36:00.002][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:36:00.004][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-01-14 12:36:00.087][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-01-14 12:36:00.158][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:36:00.159][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-01-14 12:36:00.161][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-01-14 12:36:00.164][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.170][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:00.182][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.187][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.189][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.193][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:00.194][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.194][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.200][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:00.230][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-14 12:36:00.241][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.245][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.246][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.249][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.251][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.252][private$selectFields]
biodb.TRACE[2025-01-14 12:36:00.253][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-14 12:36:00.254][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-14 12:36:00.254][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.255][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.256][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.258][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.259][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.259][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.261][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.262][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.263][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.263][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.264][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.264][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.265][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-14 12:36:00.265][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.270][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-01-14 12:36:00.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.277][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.302][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.303][private$selectFields]
biodb.TRACE[2025-01-14 12:36:00.304][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-14 12:36:00.304][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-14 12:36:00.305][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.305][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.305][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.306][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.306][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.306][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.307][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.307][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.308][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.314][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.315][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.316][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.316][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.317][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.318][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-14 12:36:00.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.322][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.326][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-14 12:36:00.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.332][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.335][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.335][private$selectFields]
biodb.TRACE[2025-01-14 12:36:00.336][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-14 12:36:00.336][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-14 12:36:00.336][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.337][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.337][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.338][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.338][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.339][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.339][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.339][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.340][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.340][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.340][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.341][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.341][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-14 12:36:00.342][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.355][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.358][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.361][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-01-14 12:36:00.362][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-14 12:36:00.362][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-14 12:36:00.367][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-01-14 12:36:00.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-01-14 12:36:00.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-14 12:36:00.370][biodb::testThat]
biodb.INFO [2025-01-14 12:36:00.371][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-01-14 12:36:00.371][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:36:00.371][biodb::testThat]
biodb.TRACE[2025-01-14 12:36:00.373][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-14 12:36:00.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-14 12:36:00.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.382][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:00.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.385][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.389][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.390][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:00.391][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:36:00.393][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:36:00.394][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-01-14 12:36:00.394][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:36:00.395][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-01-14 12:36:00.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.398][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.403][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.404][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.406][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:00.408][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:36:00.409][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:36:00.410][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-01-14 12:36:00.410][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:36:00.411][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-01-14 12:36:00.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.416][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.417][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.418][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.419][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:00.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.427][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.429][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:00.432][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-14 12:36:00.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.442][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.443][private$selectFields]
biodb.TRACE[2025-01-14 12:36:00.443][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-14 12:36:00.444][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-14 12:36:00.444][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.445][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.445][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.446][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.446][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.446][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.447][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.447][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.448][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.448][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.448][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.449][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.449][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.449][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-14 12:36:00.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.454][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-01-14 12:36:00.454][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.458][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.460][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[2025-01-14 12:36:00.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.466][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.467][private$selectFields]
biodb.TRACE[2025-01-14 12:36:00.468][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-14 12:36:00.468][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-14 12:36:00.469][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.470][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.471][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.473][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.474][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.474][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.474][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.475][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.475][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.475][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.476][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.477][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.478][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.479][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-14 12:36:00.479][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.483][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-14 12:36:00.484][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.484][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.487][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.488][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.495][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.495][private$selectFields]
biodb.TRACE[2025-01-14 12:36:00.496][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-14 12:36:00.496][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-14 12:36:00.496][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.497][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.497][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.498][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.498][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.499][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.499][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.499][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.500][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.500][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.501][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.501][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.501][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.502][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.502][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-14 12:36:00.503][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.507][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-01-14 12:36:00.508][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-14 12:36:00.510][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-14 12:36:00.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.521][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.522][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:00.527][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.528][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.531][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:00.540][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:36:00.541][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:36:00.542][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-01-14 12:36:00.543][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:36:00.543][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-01-14 12:36:00.545][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:36:00.546][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:36:00.547][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-01-14 12:36:00.547][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:36:00.548][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-01-14 12:36:00.549][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.565][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:00.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.575][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.577][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.586][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:00.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.589][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.594][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.597][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:00.599][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-14 12:36:00.600][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.600][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.605][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.609][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.609][private$selectFields]
biodb.TRACE[2025-01-14 12:36:00.610][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-14 12:36:00.610][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-14 12:36:00.610][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.611][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.611][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.612][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.612][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.612][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.613][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.613][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.613][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.614][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.614][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.615][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.615][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.616][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.616][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-14 12:36:00.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.619][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.623][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-01-14 12:36:00.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.642][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.642][private$selectFields]
biodb.TRACE[2025-01-14 12:36:00.643][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-14 12:36:00.644][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-14 12:36:00.645][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.645][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.647][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.649][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.649][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.650][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.651][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.652][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.653][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.654][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.654][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.655][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.655][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.656][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-14 12:36:00.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.658][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.664][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-14 12:36:00.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.672][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.676][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.676][private$selectFields]
biodb.TRACE[2025-01-14 12:36:00.676][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-14 12:36:00.677][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-14 12:36:00.678][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.679][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.680][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.681][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.681][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.682][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.682][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.683][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.684][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.685][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.686][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.687][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.687][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-14 12:36:00.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.691][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.692][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-01-14 12:36:00.693][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-14 12:36:00.693][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-14 12:36:00.698][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-01-14 12:36:00.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-01-14 12:36:00.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-14 12:36:00.704][biodb::testThat]
biodb.INFO [2025-01-14 12:36:00.704][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-01-14 12:36:00.705][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:36:00.706][biodb::testThat]
biodb.TRACE[2025-01-14 12:36:00.709][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-14 12:36:00.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-14 12:36:00.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.712][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.716][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.719][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.722][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:00.726][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:00.731][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:36:00.732][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:36:00.733][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-01-14 12:36:00.734][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:36:00.735][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-01-14 12:36:00.738][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.744][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.746][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.749][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:00.752][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:36:00.754][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:36:00.755][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-01-14 12:36:00.756][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:36:00.758][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-01-14 12:36:00.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.771][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.772][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.773][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.774][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:00.777][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.787][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.791][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:00.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:00.797][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-14 12:36:00.799][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.814][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.815][private$selectFields]
biodb.TRACE[2025-01-14 12:36:00.815][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-14 12:36:00.815][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-14 12:36:00.816][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.817][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.817][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.818][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.819][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.820][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.820][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.821][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.821][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.822][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.822][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.823][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.823][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.824][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.824][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.825][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-14 12:36:00.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.828][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.833][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-01-14 12:36:00.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.840][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.848][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.849][private$selectFields]
biodb.TRACE[2025-01-14 12:36:00.850][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-14 12:36:00.851][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-14 12:36:00.852][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.852][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.853][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.855][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.856][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.858][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.858][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.859][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.860][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.861][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.862][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.863][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.865][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.866][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-14 12:36:00.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.877][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-14 12:36:00.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:00.889][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.898][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.898][private$selectFields]
biodb.TRACE[2025-01-14 12:36:00.899][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-14 12:36:00.900][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-14 12:36:00.901][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.902][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.903][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.904][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.905][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.906][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.907][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.908][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.909][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.910][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:00.911][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.912][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.913][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.914][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-14 12:36:00.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.922][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:00.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.925][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-01-14 12:36:00.926][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-14 12:36:00.927][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-14 12:36:00.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:00.960][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:00.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:00.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:00.968][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:00.969][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:00.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:00.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:00.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:00.977][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:00.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:00.980][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:36:00.984][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:36:00.985][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-01-14 12:36:00.987][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:36:00.988][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-01-14 12:36:00.992][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:36:00.996][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:36:00.997][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-01-14 12:36:00.998][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:36:01.000][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-01-14 12:36:01.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:01.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:01.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:01.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:01.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:01.012][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:01.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:01.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:01.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:01.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:01.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:01.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.022][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:01.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:01.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:01.025][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:01.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:01.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:01.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:01.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:01.034][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:01.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:01.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:01.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:01.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:01.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:01.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:01.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:01.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:01.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:01.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:01.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:01.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:01.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:01.055][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:01.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:01.057][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:01.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:01.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:01.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:01.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:01.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:01.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:01.067][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-14 12:36:01.069][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:01.070][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:01.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:01.083][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:01.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:01.086][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:01.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:01.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.094][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:01.095][private$selectFields]
biodb.TRACE[2025-01-14 12:36:01.096][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-14 12:36:01.097][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-14 12:36:01.097][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:01.098][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.099][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.101][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.101][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.102][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.103][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.104][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.105][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:01.106][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:01.106][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.107][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.109][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.110][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-14 12:36:01.110][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.114][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.122][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-01-14 12:36:01.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:01.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:01.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:01.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:01.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:01.133][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:01.134][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.TRACE[2025-01-14 12:36:01.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.143][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:01.144][private$selectFields]
biodb.TRACE[2025-01-14 12:36:01.145][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-14 12:36:01.146][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-14 12:36:01.146][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:01.147][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.148][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.149][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.150][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.150][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.151][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.152][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.153][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.154][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:01.154][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:01.155][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.156][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.157][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.158][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.158][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-14 12:36:01.159][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.166][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.170][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-14 12:36:01.171][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:01.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:01.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:01.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:01.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:01.180][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:01.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:01.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.189][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:01.190][private$selectFields]
biodb.TRACE[2025-01-14 12:36:01.190][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-14 12:36:01.191][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-14 12:36:01.192][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:01.193][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.194][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.195][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.196][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.196][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.197][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.199][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.200][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:01.201][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-14 12:36:01.202][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.202][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.204][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.205][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-14 12:36:01.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.216][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-01-14 12:36:01.217][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-14 12:36:01.218][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-14 12:36:01.238][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-01-14 12:36:01.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-01-14 12:36:01.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-14 12:36:01.245][biodb::testThat]
biodb.INFO [2025-01-14 12:36:01.246][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-01-14 12:36:01.247][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:36:01.248][biodb::testThat]
biodb.DEBUG[2025-01-14 12:36:01.250][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-01-14 12:36:01.251][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:36:01.252][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-01-14 12:36:01.253][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:36:01.254][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:36:01.255][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:36:01.256][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:36:01.257][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:36:01.258][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:36:01.261][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:01.262][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:01.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:01.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:01.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:01.270][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:01.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:01.272][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-01-14 12:36:01.275][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:36:01.276][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:36:01.277][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-01-14 12:36:01.373][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-01-14 12:36:01.460][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:36:01.462][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-01-14 12:36:01.466][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-01-14 12:36:01.468][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-01-14 12:36:01.470][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:36:01.471][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:36:01.473][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:36:01.475][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:01.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:01.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:01.482][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:01.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:01.484][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:01.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:01.492][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:01.494][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:01.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.495][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:01.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:01.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.500][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:36:01.501][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:36:01.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.503][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.504][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:36:01.505][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:36:01.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.506][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.508][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:36:01.508][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:36:01.509][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.510][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.511][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:36:01.512][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:36:01.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.513][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.514][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:36:01.515][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:36:01.516][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.517][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.518][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:36:01.519][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:01.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.520][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.521][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:01.522][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:01.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.524][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.525][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:36:01.526][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:36:01.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.527][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.528][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:36:01.529][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:36:01.530][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.531][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.532][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:36:01.533][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:36:01.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.534][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:01.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:01.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:01.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:01.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:01.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:01.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:01.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:01.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:01.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:01.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:01.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:01.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:01.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:01.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:01.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:01.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:01.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:01.569][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-01-14 12:36:01.570][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-01-14 12:36:01.580][biodb::testThat]
biodb.INFO [2025-01-14 12:36:01.581][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-01-14 12:36:01.582][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:36:01.583][biodb::testThat]
biodb.DEBUG[2025-01-14 12:36:01.604][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-01-14 12:36:01.606][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-01-14 12:36:01.607][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-01-14 12:36:01.608][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-01-14 12:36:01.610][cch$loadFileContent] file.exist = [3]: "FALSE, TRUE, FALSE".
biodb.TRACE[2025-01-14 12:36:01.611][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml".
biodb.DEBUG[2025-01-14 12:36:01.612][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:36:01.613][conn$getEntryContent] 2 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:36:01.614][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:36:01.615][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:36:01.618][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:01.619][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:01.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:01.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:01.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:01.627][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:01.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:01.629][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-01-14 12:36:01.632][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:36:01.632][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:36:01.634][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-01-14 12:36:01.712][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-01-14 12:36:01.798][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:36:01.800][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-01-14 12:36:01.804][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-01-14 12:36:01.805][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:01.806][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:01.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:01.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:01.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:01.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:01.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:01.816][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-01-14 12:36:01.818][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:36:01.819][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:36:01.820][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-01-14 12:36:01.898][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-01-14 12:36:01.982][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:36:01.984][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-01-14 12:36:01.988][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-01-14 12:36:01.991][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-01-14 12:36:01.993][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:36:01.994][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-01-14 12:36:01.995][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-01-14 12:36:01.996][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:01.997][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:01.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:02.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:02.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:02.005][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:02.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:02.009][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.010][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.012][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.016][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:36:02.017][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:36:02.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.019][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.020][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:36:02.021][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:36:02.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.022][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.023][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:36:02.024][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:36:02.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.026][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.027][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:36:02.028][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:36:02.028][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.029][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.030][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:36:02.031][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:36:02.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.033][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.034][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:36:02.034][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:02.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.036][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.037][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:02.038][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:02.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.039][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.040][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:36:02.041][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:36:02.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.043][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.044][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:36:02.045][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:36:02.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.046][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.047][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:36:02.048][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:36:02.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.050][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:02.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:02.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.054][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:02.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:02.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:02.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:02.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:02.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:02.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:02.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:02.081][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:02.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:02.083][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:02.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:02.086][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.087][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.089][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.094][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:36:02.095][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:36:02.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.096][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.097][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:36:02.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:36:02.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.101][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:36:02.102][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:36:02.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.103][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.105][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:36:02.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:36:02.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.108][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:36:02.109][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:36:02.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.110][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.111][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:36:02.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:36:02.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.115][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:36:02.116][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:36:02.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.118][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.119][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:36:02.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:36:02.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.122][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:36:02.123][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:36:02.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.124][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.126][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:36:02.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:36:02.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.129][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:36:02.130][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:02.131][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.131][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.132][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:36:02.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:02.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.136][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:02.137][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:02.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.138][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:02.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:02.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.143][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:36:02.144][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:36:02.144][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.145][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.146][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:36:02.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:36:02.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.150][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:36:02.151][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:36:02.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.152][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.153][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:36:02.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:36:02.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.157][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:36:02.157][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:36:02.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.159][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.160][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:36:02.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:36:02.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:02.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:02.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:02.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:02.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:02.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:02.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:02.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:02.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:02.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:02.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:02.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:02.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:02.199][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[2025-01-14 12:36:02.201][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.202][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.204][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.209][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:36:02.210][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:36:02.211][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.211][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.213][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:36:02.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:36:02.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.216][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:36:02.217][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:36:02.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.218][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.220][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:36:02.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:36:02.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.223][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:36:02.224][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:36:02.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.225][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.226][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:36:02.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:36:02.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.230][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:36:02.232][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:36:02.233][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.234][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.248][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:36:02.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:36:02.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.251][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:36:02.251][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:36:02.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.252][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.253][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:36:02.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:36:02.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.254][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:36:02.254][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:02.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.255][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.256][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:36:02.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:02.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.260][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:02.261][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:02.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.262][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:02.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:02.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.267][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:36:02.267][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:36:02.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.269][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.270][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:36:02.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:36:02.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.274][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:36:02.275][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:36:02.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.277][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.278][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:36:02.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:36:02.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.281][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:36:02.282][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:36:02.283][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.283][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.284][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:36:02.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:36:02.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:02.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:02.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.291][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:02.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:02.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:02.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:02.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:02.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:02.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:02.341][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-01-14 12:36:02.341][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-01-14 12:36:02.342][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-01-14 12:36:02.358][biodb::testThat]
biodb.INFO [2025-01-14 12:36:02.359][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-01-14 12:36:02.360][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:36:02.361][biodb::testThat]
biodb.INFO [2025-01-14 12:36:02.387][biodb::testThat]
biodb.INFO [2025-01-14 12:36:02.388][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-01-14 12:36:02.389][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:36:02.390][biodb::testThat]
biodb.INFO [2025-01-14 12:36:02.400][biodb::testThat]
biodb.INFO [2025-01-14 12:36:02.401][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-01-14 12:36:02.402][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:36:02.403][biodb::testThat]
biodb.DEBUG[2025-01-14 12:36:02.405][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[2025-01-14 12:36:02.409][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:36:02.410][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:36:02.412][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-01-14 12:36:02.620][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-01-14 12:36:02.794][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:36:02.797][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-01-14 12:36:02.801][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-01-14 12:36:02.814][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:36:02.815][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:36:02.816][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.817][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:02.818][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:02.819][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:02.819][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:02.820][ef$get] fields variable is a list.
biodb.INFO [2025-01-14 12:36:02.822][biodb::testThat]
biodb.INFO [2025-01-14 12:36:02.823][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2025-01-14 12:36:02.823][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:36:02.824][biodb::testThat]
biodb.ERROR[2025-01-14 12:36:02.839][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-01-14 12:36:02.859][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-01-14 12:36:02.875][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-14 12:36:02.877][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-01-14 12:36:02.878][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-01-14 12:36:02.879][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-14 12:36:02.879][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:02.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:02.881][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:02.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:02.882][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:02.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-14 12:36:02.894][biodb::testContext]
biodb.INFO [2025-01-14 12:36:02.895][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-14 12:36:02.896][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-01-14 12:36:02.897][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-14 12:36:02.897][biodb::testContext]
biodb.INFO [2025-01-14 12:36:02.900][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-14 12:36:02.901][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-01-14 12:36:02.907][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-14 12:36:02.908][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-14 12:36:02.909][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-14 12:36:02.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:02.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:02.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:02.912][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-14 12:36:02.913][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-14 12:36:02.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:02.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:02.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:02.916][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-14 12:36:02.917][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-14 12:36:02.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:02.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:02.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:02.920][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-14 12:36:02.921][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-14 12:36:02.922][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-14 12:36:02.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:02.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:02.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:02.925][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-14 12:36:02.925][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-14 12:36:02.926][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-14 12:36:02.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:02.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:02.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:02.929][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-14 12:36:02.930][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-14 12:36:02.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:02.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:02.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:02.933][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-14 12:36:02.934][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-14 12:36:02.935][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-14 12:36:02.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:02.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:02.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:02.938][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-14 12:36:02.939][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-14 12:36:02.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:02.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:02.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:02.942][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-14 12:36:02.943][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-14 12:36:02.943][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-14 12:36:02.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:02.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:02.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:02.946][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-14 12:36:02.947][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-14 12:36:02.948][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-14 12:36:02.949][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-14 12:36:02.957][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-14 12:36:02.962][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-14 12:36:02.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:02.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:02.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:02.966][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-14 12:36:02.967][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-14 12:36:02.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:02.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:02.969][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[2025-01-14 12:36:02.970][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-14 12:36:02.971][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-14 12:36:02.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:02.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:02.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:02.974][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-14 12:36:02.975][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-14 12:36:02.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:02.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:02.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:02.977][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-14 12:36:02.978][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-14 12:36:02.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:02.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:02.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:02.981][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-14 12:36:02.982][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-14 12:36:02.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:02.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:02.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:02.985][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-14 12:36:02.986][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-14 12:36:03.000][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-14 12:36:03.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.004][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-14 12:36:03.004][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-14 12:36:03.005][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-14 12:36:03.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.008][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-14 12:36:03.010][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:03.011][self$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[2025-01-14 12:36:03.012][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:03.013][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-14 12:36:03.013][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:03.014][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-14 12:36:03.015][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:03.016][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-14 12:36:03.016][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-14 12:36:03.017][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-14 12:36:03.018][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:03.019][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-14 12:36:03.020][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-14 12:36:03.020][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:03.021][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:03.022][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-14 12:36:03.022][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-14 12:36:03.022][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-14 12:36:03.022][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-14 12:36:03.022][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-14 12:36:03.023][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-14 12:36:03.024][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:03.024][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:03.025][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-14 12:36:03.026][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:03.027][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:03.027][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-14 12:36:03.028][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:03.029][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-14 12:36:03.029][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-14 12:36:03.030][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:03.031][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:03.032][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-14 12:36:03.034][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:03.034][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-14 12:36:03.035][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:03.036][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-14 12:36:03.037][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:03.038][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-14 12:36:03.038][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:03.039][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-14 12:36:03.040][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-14 12:36:03.041][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-14 12:36:03.041][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:03.042][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-14 12:36:03.043][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-14 12:36:03.044][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:03.045][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:03.045][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-14 12:36:03.045][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-14 12:36:03.045][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-14 12:36:03.045][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-14 12:36:03.045][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-14 12:36:03.046][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-14 12:36:03.047][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:03.048][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:03.048][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-14 12:36:03.049][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:03.050][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:03.051][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-14 12:36:03.051][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:03.052][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-14 12:36:03.053][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-14 12:36:03.054][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:03.054][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:03.055][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-14 12:36:03.057][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:03.058][self$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[2025-01-14 12:36:03.058][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:03.059][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-14 12:36:03.060][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:03.061][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-14 12:36:03.062][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:03.062][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-14 12:36:03.063][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-14 12:36:03.064][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-14 12:36:03.065][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:03.066][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-14 12:36:03.066][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-14 12:36:03.067][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:03.068][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:03.069][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:03.069][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-14 12:36:03.070][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:03.071][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:03.072][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-14 12:36:03.073][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:03.073][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:03.074][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-14 12:36:03.075][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:03.076][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-14 12:36:03.076][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-14 12:36:03.077][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:03.078][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:03.079][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-14 12:36:03.080][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:03.081][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-14 12:36:03.082][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:03.083][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-14 12:36:03.084][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:03.086][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-14 12:36:03.087][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:03.087][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-14 12:36:03.088][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-14 12:36:03.089][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-14 12:36:03.090][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:03.091][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-14 12:36:03.092][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-14 12:36:03.093][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:03.094][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:03.095][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:03.096][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-14 12:36:03.096][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:03.097][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:03.098][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-14 12:36:03.099][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:03.100][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:03.101][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-14 12:36:03.102][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:03.103][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-14 12:36:03.104][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-14 12:36:03.105][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:03.106][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:03.107][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-14 12:36:03.108][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.131][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[2025-01-14 12:36:03.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.139][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[2025-01-14 12:36:03.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.143][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[2025-01-14 12:36:03.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.150][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.DEBUG[2025-01-14 12:36:03.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.153][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[2025-01-14 12:36:03.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.157][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[2025-01-14 12:36:03.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.160][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[2025-01-14 12:36:03.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.169][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[2025-01-14 12:36:03.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.173][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[2025-01-14 12:36:03.174][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-14 12:36:03.175][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-14 12:36:03.176][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-14 12:36:03.178][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-14 12:36:03.179][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-14 12:36:03.180][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-14 12:36:03.182][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-14 12:36:03.183][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-14 12:36:03.184][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-14 12:36:03.186][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-14 12:36:03.187][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-14 12:36:03.188][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-14 12:36:03.190][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-14 12:36:03.191][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-14 12:36:03.192][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-14 12:36:03.193][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-14 12:36:03.194][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-14 12:36:03.196][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-14 12:36:03.197][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-14 12:36:03.198][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-14 12:36:03.199][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-14 12:36:03.200][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-14 12:36:03.201][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-14 12:36:03.203][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-14 12:36:03.204][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-14 12:36:03.205][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-14 12:36:03.206][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-14 12:36:03.207][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-14 12:36:03.209][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-14 12:36:03.210][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-14 12:36:03.211][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-14 12:36:03.212][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-14 12:36:03.214][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-14 12:36:03.215][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-14 12:36:03.216][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-14 12:36:03.217][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-14 12:36:03.218][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-14 12:36:03.220][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-14 12:36:03.221][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-14 12:36:03.222][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-14 12:36:03.223][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-14 12:36:03.224][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-14 12:36:03.226][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-14 12:36:03.227][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-14 12:36:03.228][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-14 12:36:03.229][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-14 12:36:03.231][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-14 12:36:03.232][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-14 12:36:03.234][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-14 12:36:03.235][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-14 12:36:03.236][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-14 12:36:03.237][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-14 12:36:03.239][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-14 12:36:03.240][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-14 12:36:03.241][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-14 12:36:03.242][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-14 12:36:03.243][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-14 12:36:03.245][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-14 12:36:03.246][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-14 12:36:03.247][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-14 12:36:03.248][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-14 12:36:03.249][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-14 12:36:03.250][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-14 12:36:03.252][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-14 12:36:03.260][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-14 12:36:03.262][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-14 12:36:03.263][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-14 12:36:03.264][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-14 12:36:03.265][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-14 12:36:03.266][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-14 12:36:03.268][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-14 12:36:03.269][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-14 12:36:03.270][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-14 12:36:03.271][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-14 12:36:03.272][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-14 12:36:03.273][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-14 12:36:03.275][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-14 12:36:03.276][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-14 12:36:03.277][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-14 12:36:03.278][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-14 12:36:03.279][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-14 12:36:03.281][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-14 12:36:03.282][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-14 12:36:03.284][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-14 12:36:03.285][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-14 12:36:03.286][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-14 12:36:03.287][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.289][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.294][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[2025-01-14 12:36:03.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.309][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[2025-01-14 12:36:03.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.339][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[2025-01-14 12:36:03.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.356][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[2025-01-14 12:36:03.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.366][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[2025-01-14 12:36:03.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:03.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.378][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-01-14 12:36:03.380][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-01-14 12:36:03.382][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:03.383][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-14 12:36:03.384][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:03.385][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-14 12:36:03.386][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:03.386][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-14 12:36:03.387][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:03.388][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-01-14 12:36:03.389][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-14 12:36:03.390][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-14 12:36:03.390][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:03.391][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-01-14 12:36:03.392][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-14 12:36:03.393][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-01-14 12:36:03.393][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-01-14 12:36:03.393][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-01-14 12:36:03.393][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-01-14 12:36:03.393][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-01-14 12:36:03.393][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-01-14 12:36:03.393][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-01-14 12:36:03.393][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-01-14 12:36:03.393][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-01-14 12:36:03.393][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-01-14 12:36:03.393][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-01-14 12:36:03.394][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:03.395][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-14 12:36:03.395][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-14 12:36:03.395][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-14 12:36:03.396][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-14 12:36:03.397][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:03.397][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:03.398][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-14 12:36:03.399][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:03.400][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:03.401][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-14 12:36:03.401][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:36:03.401][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-01-14 12:36:03.402][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-14 12:36:03.403][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-14 12:36:03.404][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:03.405][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-01-14 12:36:03.405][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-01-14 12:36:03.406][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-14 12:36:03.407][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-14 12:36:03.409][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-01-14 12:36:03.410][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-14 12:36:03.412][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-14 12:36:03.414][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-14 12:36:03.417][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-01-14 12:36:03.418][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-01-14 12:36:03.419][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-01-14 12:36:03.421][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-01-14 12:36:03.422][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-14 12:36:03.423][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-14 12:36:03.424][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-01-14 12:36:03.425][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-01-14 12:36:03.426][biodb::testThat]
biodb.INFO [2025-01-14 12:36:03.427][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2025-01-14 12:36:03.428][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:36:03.429][biodb::testThat]
biodb.DEBUG[2025-01-14 12:36:03.432][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-01-14 12:36:03.436][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:36:03.438][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-01-14 12:36:03.439][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:36:03.440][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-01-14 12:36:03.444][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:36:03.448][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:36:03.449][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-01-14 12:36:03.450][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:36:03.452][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-01-14 12:36:03.454][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:03.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.465][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.468][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:36:03.472][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:36:03.473][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-01-14 12:36:03.474][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:36:03.476][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-01-14 12:36:03.478][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:03.479][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.487][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:03.508][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.523][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:36:03.527][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:36:03.529][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-01-14 12:36:03.530][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:36:03.531][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-01-14 12:36:03.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:03.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.540][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.542][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.545][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:36:03.548][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:36:03.549][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-01-14 12:36:03.551][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:36:03.552][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-01-14 12:36:03.554][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:03.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.561][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.563][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:03.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.578][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:36:03.582][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:36:03.590][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-01-14 12:36:03.592][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:36:03.593][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-01-14 12:36:03.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:03.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.602][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.603][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.606][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:36:03.609][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:36:03.610][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-01-14 12:36:03.612][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:36:03.613][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-01-14 12:36:03.616][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:03.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.627][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:36:03.630][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:36:03.631][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2025-01-14 12:36:03.632][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:36:03.634][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2025-01-14 12:36:03.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:03.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-14 12:36:03.651][biodb::testThat]
biodb.INFO [2025-01-14 12:36:03.652][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2025-01-14 12:36:03.653][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:36:03.654][biodb::testThat]
biodb.DEBUG[2025-01-14 12:36:03.657][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:36:03.661][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:36:03.662][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:36:03.664][private$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[2025-01-14 12:36:03.745][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[2025-01-14 12:36:03.832][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:36:03.835][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-01-14 12:36:03.839][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-01-14 12:36:03.842][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:03.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:03.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:03.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:03.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:03.850][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:03.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:03.855][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[2025-01-14 12:36:03.858][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:36:03.859][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:36:03.861][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-01-14 12:36:03.945][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-01-14 12:36:04.040][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:36:04.042][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-01-14 12:36:04.047][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-01-14 12:36:04.051][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:04.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:04.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:04.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-14 12:36:04.069][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-14 12:36:04.071][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-01-14 12:36:04.072][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-01-14 12:36:04.073][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-14 12:36:04.075][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:04.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:04.077][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.079][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-14 12:36:04.085][biodb::testContext]
biodb.INFO [2025-01-14 12:36:04.087][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-14 12:36:04.088][biodb::testContext] Test context - Test web services
biodb.INFO [2025-01-14 12:36:04.088][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-14 12:36:04.089][biodb::testContext]
biodb.INFO [2025-01-14 12:36:04.092][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-14 12:36:04.093][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-01-14 12:36:04.098][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-14 12:36:04.099][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-14 12:36:04.100][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-14 12:36:04.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.103][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.DEBUG[2025-01-14 12:36:04.103][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-14 12:36:04.104][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-14 12:36:04.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.107][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-14 12:36:04.108][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-14 12:36:04.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.110][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[2025-01-14 12:36:04.111][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-14 12:36:04.112][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-14 12:36:04.112][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-14 12:36:04.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.115][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-14 12:36:04.116][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-14 12:36:04.117][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-14 12:36:04.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.119][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[2025-01-14 12:36:04.120][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-14 12:36:04.121][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-14 12:36:04.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.124][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-14 12:36:04.124][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-14 12:36:04.125][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-14 12:36:04.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.128][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-14 12:36:04.129][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-14 12:36:04.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.132][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-14 12:36:04.133][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-14 12:36:04.134][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-14 12:36:04.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.137][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-14 12:36:04.137][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-14 12:36:04.138][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-14 12:36:04.139][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-14 12:36:04.140][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-14 12:36:04.140][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-14 12:36:04.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.143][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-14 12:36:04.144][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-14 12:36:04.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.147][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-14 12:36:04.148][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-14 12:36:04.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.151][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-14 12:36:04.152][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-14 12:36:04.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.157][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-14 12:36:04.158][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-14 12:36:04.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.162][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-14 12:36:04.163][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-14 12:36:04.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.165][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-14 12:36:04.166][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-14 12:36:04.183][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-14 12:36:04.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.187][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-14 12:36:04.188][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-14 12:36:04.188][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-14 12:36:04.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.192][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-14 12:36:04.193][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:04.194][self$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[2025-01-14 12:36:04.195][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.196][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-14 12:36:04.197][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.197][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.198][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:04.199][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.200][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-14 12:36:04.201][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-14 12:36:04.201][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.202][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-14 12:36:04.203][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-14 12:36:04.204][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:04.205][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.205][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-14 12:36:04.205][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-14 12:36:04.205][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-14 12:36:04.205][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-14 12:36:04.205][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-14 12:36:04.206][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-14 12:36:04.207][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:04.208][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:04.209][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-14 12:36:04.209][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:04.210][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:04.211][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.212][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:04.212][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-14 12:36:04.213][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-14 12:36:04.214][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:04.215][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:04.216][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-14 12:36:04.217][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:04.218][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-14 12:36:04.219][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.220][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-14 12:36:04.221][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.222][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.223][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:04.223][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.224][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-14 12:36:04.225][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-14 12:36:04.226][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.227][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-14 12:36:04.227][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-14 12:36:04.228][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:04.229][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.230][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-14 12:36:04.230][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-14 12:36:04.230][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-14 12:36:04.230][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-14 12:36:04.230][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-14 12:36:04.232][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-14 12:36:04.233][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:04.234][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:04.235][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-14 12:36:04.236][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:04.236][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:04.237][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.238][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:04.239][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-14 12:36:04.240][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-14 12:36:04.240][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:04.241][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:04.242][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-14 12:36:04.244][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.245][self$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[2025-01-14 12:36:04.246][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.247][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-14 12:36:04.248][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.248][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.249][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:04.250][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.251][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-14 12:36:04.252][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-14 12:36:04.252][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:04.253][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-14 12:36:04.254][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-14 12:36:04.255][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:04.256][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.256][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:04.257][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-14 12:36:04.258][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:04.259][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:04.260][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-14 12:36:04.260][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:04.261][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:04.262][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.263][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:04.263][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-14 12:36:04.264][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-14 12:36:04.265][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:04.266][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:04.267][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-14 12:36:04.269][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.270][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-14 12:36:04.271][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.271][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-14 12:36:04.272][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.273][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.281][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:04.289][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.290][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-14 12:36:04.291][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-14 12:36:04.292][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:04.292][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-14 12:36:04.293][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-14 12:36:04.294][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:04.295][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.295][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:04.296][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-14 12:36:04.297][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:04.298][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:04.299][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-14 12:36:04.299][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:04.300][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:04.301][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.302][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:04.302][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-14 12:36:04.303][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-14 12:36:04.304][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:04.305][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:04.306][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-14 12:36:04.306][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.326][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[2025-01-14 12:36:04.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.333][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[2025-01-14 12:36:04.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.340][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[2025-01-14 12:36:04.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.347][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[2025-01-14 12:36:04.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.369][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-14 12:36:04.370][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-14 12:36:04.372][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-14 12:36:04.373][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-14 12:36:04.374][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-14 12:36:04.375][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-14 12:36:04.376][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-14 12:36:04.378][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-14 12:36:04.379][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-14 12:36:04.380][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-14 12:36:04.381][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-14 12:36:04.382][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-14 12:36:04.384][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-14 12:36:04.385][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-14 12:36:04.386][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-14 12:36:04.387][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-14 12:36:04.389][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-14 12:36:04.390][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-14 12:36:04.391][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-14 12:36:04.392][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-14 12:36:04.393][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-14 12:36:04.394][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-14 12:36:04.395][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-14 12:36:04.397][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-14 12:36:04.398][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-14 12:36:04.399][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-14 12:36:04.400][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-14 12:36:04.401][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-14 12:36:04.403][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-14 12:36:04.405][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-14 12:36:04.407][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-14 12:36:04.408][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-14 12:36:04.410][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-14 12:36:04.411][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-14 12:36:04.412][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-14 12:36:04.413][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-14 12:36:04.415][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-14 12:36:04.416][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-14 12:36:04.417][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-14 12:36:04.418][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-14 12:36:04.420][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-14 12:36:04.421][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-14 12:36:04.422][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-14 12:36:04.423][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-14 12:36:04.425][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-14 12:36:04.426][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-14 12:36:04.427][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-14 12:36:04.428][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-14 12:36:04.430][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-14 12:36:04.431][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-14 12:36:04.432][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-14 12:36:04.433][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-14 12:36:04.434][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-14 12:36:04.436][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-14 12:36:04.437][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-14 12:36:04.438][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-14 12:36:04.439][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-14 12:36:04.440][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-14 12:36:04.442][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-14 12:36:04.443][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-14 12:36:04.444][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-14 12:36:04.445][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-14 12:36:04.446][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-14 12:36:04.448][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-14 12:36:04.449][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-14 12:36:04.450][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-14 12:36:04.451][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-14 12:36:04.452][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-14 12:36:04.453][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-14 12:36:04.455][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-14 12:36:04.456][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-14 12:36:04.457][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-14 12:36:04.458][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-14 12:36:04.459][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-14 12:36:04.460][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-14 12:36:04.461][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-14 12:36:04.463][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-14 12:36:04.464][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-14 12:36:04.465][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-14 12:36:04.467][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-14 12:36:04.468][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-14 12:36:04.470][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-14 12:36:04.471][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-14 12:36:04.472][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-14 12:36:04.474][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-14 12:36:04.475][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-14 12:36:04.476][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.478][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:04.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:04.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:04.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:04.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:04.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:04.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:04.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:04.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:04.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:04.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:04.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:04.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:04.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:04.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.513][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[2025-01-14 12:36:04.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:04.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:04.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:04.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:04.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:04.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:04.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.528][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[2025-01-14 12:36:04.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:04.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:04.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:04.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:04.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.538][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[2025-01-14 12:36:04.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:04.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:04.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:04.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:04.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:04.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:04.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.553][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[2025-01-14 12:36:04.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:04.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:04.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:04.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:04.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.574][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-01-14 12:36:04.576][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-01-14 12:36:04.577][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:04.578][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.579][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.580][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-14 12:36:04.581][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.581][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.582][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.583][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-01-14 12:36:04.584][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-14 12:36:04.585][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-14 12:36:04.585][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.586][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-01-14 12:36:04.587][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-14 12:36:04.588][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-01-14 12:36:04.588][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-01-14 12:36:04.588][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-01-14 12:36:04.588][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-01-14 12:36:04.588][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-01-14 12:36:04.588][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-01-14 12:36:04.588][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-01-14 12:36:04.588][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-01-14 12:36:04.588][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-01-14 12:36:04.588][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-01-14 12:36:04.588][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-01-14 12:36:04.589][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:04.590][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-14 12:36:04.590][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-14 12:36:04.590][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-14 12:36:04.590][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-14 12:36:04.591][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:04.592][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:04.593][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-14 12:36:04.593][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:04.594][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:04.595][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.596][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:36:04.596][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-01-14 12:36:04.596][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-14 12:36:04.597][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-14 12:36:04.598][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.599][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-01-14 12:36:04.599][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-01-14 12:36:04.600][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-14 12:36:04.601][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-14 12:36:04.603][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-01-14 12:36:04.604][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-14 12:36:04.605][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-14 12:36:04.607][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-14 12:36:04.610][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-01-14 12:36:04.611][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-01-14 12:36:04.612][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-01-14 12:36:04.613][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-01-14 12:36:04.615][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-14 12:36:04.615][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-14 12:36:04.616][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-01-14 12:36:04.617][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-01-14 12:36:04.619][biodb::testThat]
biodb.INFO [2025-01-14 12:36:04.619][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-01-14 12:36:04.620][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:36:04.621][biodb::testThat]
biodb.DEBUG[2025-01-14 12:36:04.624][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-01-14 12:36:04.628][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:36:04.629][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-01-14 12:36:04.631][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:36:04.632][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-01-14 12:36:04.636][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-14 12:36:04.639][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:36:04.641][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:36:04.642][private$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[2025-01-14 12:36:04.725][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[2025-01-14 12:36:04.807][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:36:04.809][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-01-14 12:36:04.813][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-01-14 12:36:04.823][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-14 12:36:04.825][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-01-14 12:36:04.826][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-01-14 12:36:04.827][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-14 12:36:04.827][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:04.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:04.829][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:04.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:04.830][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-14 12:36:04.835][biodb::testContext]
biodb.INFO [2025-01-14 12:36:04.836][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-14 12:36:04.837][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-01-14 12:36:04.838][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-14 12:36:04.839][biodb::testContext]
biodb.INFO [2025-01-14 12:36:04.841][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-14 12:36:04.843][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-01-14 12:36:04.849][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-14 12:36:04.850][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-14 12:36:04.851][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-14 12:36:04.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.855][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-14 12:36:04.856][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-14 12:36:04.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.859][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-14 12:36:04.860][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-14 12:36:04.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.863][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-14 12:36:04.864][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-14 12:36:04.865][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-14 12:36:04.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.869][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-14 12:36:04.870][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-14 12:36:04.870][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-14 12:36:04.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.873][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-14 12:36:04.874][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-14 12:36:04.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.877][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-14 12:36:04.878][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-14 12:36:04.879][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-14 12:36:04.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.882][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-14 12:36:04.882][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-14 12:36:04.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.885][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-14 12:36:04.886][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-14 12:36:04.887][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-14 12:36:04.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.890][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-14 12:36:04.891][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-14 12:36:04.891][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-14 12:36:04.892][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-14 12:36:04.893][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-14 12:36:04.894][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-14 12:36:04.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.897][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-14 12:36:04.898][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-14 12:36:04.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.901][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-14 12:36:04.902][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-14 12:36:04.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.906][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-14 12:36:04.906][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-14 12:36:04.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.909][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-14 12:36:04.910][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-14 12:36:04.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.913][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-14 12:36:04.914][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-14 12:36:04.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.917][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-14 12:36:04.918][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-14 12:36:04.933][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-14 12:36:04.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.937][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-14 12:36:04.938][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-14 12:36:04.939][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-14 12:36:04.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:04.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:04.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:04.942][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-14 12:36:04.944][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:04.945][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-14 12:36:04.946][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.946][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-14 12:36:04.947][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.948][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.949][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:04.950][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.950][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-14 12:36:04.951][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-14 12:36:04.952][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.953][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-14 12:36:04.954][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-14 12:36:04.955][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:04.955][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.956][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-14 12:36:04.956][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-14 12:36:04.956][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-14 12:36:04.956][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-14 12:36:04.956][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-14 12:36:04.957][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-14 12:36:04.958][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:04.959][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:04.959][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-14 12:36:04.960][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:04.961][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:04.962][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.963][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:04.963][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-14 12:36:04.964][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-14 12:36:04.965][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:04.966][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:04.967][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-14 12:36:04.969][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:04.970][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-14 12:36:04.970][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.971][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-14 12:36:04.972][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.973][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.974][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:04.974][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.975][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-14 12:36:04.976][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-14 12:36:04.977][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.978][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-14 12:36:04.978][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-14 12:36:04.979][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:04.980][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.981][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-14 12:36:04.981][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-14 12:36:04.981][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-14 12:36:04.981][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-14 12:36:04.981][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-14 12:36:04.982][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-14 12:36:04.983][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:04.983][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:04.984][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-14 12:36:04.985][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:04.986][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:04.986][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.987][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:04.988][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-14 12:36:04.989][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-14 12:36:04.989][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:04.990][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:04.991][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-14 12:36:04.993][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.994][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-14 12:36:04.994][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.995][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-14 12:36:04.996][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:04.997][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.998][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:04.999][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-14 12:36:04.999][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-14 12:36:05.000][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-14 12:36:05.002][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:05.002][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-14 12:36:05.003][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-14 12:36:05.004][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:05.004][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:05.005][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:05.005][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-14 12:36:05.006][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:05.007][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:05.007][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-14 12:36:05.008][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:05.009][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:05.010][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-14 12:36:05.011][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:05.011][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-14 12:36:05.012][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-14 12:36:05.013][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:05.014][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:05.015][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-14 12:36:05.016][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:05.017][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-14 12:36:05.018][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:05.019][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-14 12:36:05.020][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:05.020][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-14 12:36:05.021][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:05.022][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-14 12:36:05.023][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-14 12:36:05.024][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-14 12:36:05.024][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:05.025][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-14 12:36:05.026][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-14 12:36:05.027][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:05.028][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:05.029][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:05.029][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-14 12:36:05.030][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:05.031][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:05.032][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-14 12:36:05.032][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:05.033][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:05.034][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-14 12:36:05.034][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:05.036][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-14 12:36:05.037][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-14 12:36:05.048][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:05.049][self$setPropertyValue]
biodb.DEBUG[2025-01-14 12:36:05.050][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-14 12:36:05.051][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.052][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[2025-01-14 12:36:05.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.062][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[2025-01-14 12:36:05.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.073][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[2025-01-14 12:36:05.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.080][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[2025-01-14 12:36:05.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.083][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[2025-01-14 12:36:05.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.100][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[2025-01-14 12:36:05.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.104][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[2025-01-14 12:36:05.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.107][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[2025-01-14 12:36:05.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.112][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-14 12:36:05.113][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-14 12:36:05.114][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-14 12:36:05.116][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-14 12:36:05.117][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-14 12:36:05.118][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-14 12:36:05.119][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-14 12:36:05.120][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-14 12:36:05.121][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-14 12:36:05.123][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-14 12:36:05.124][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-14 12:36:05.125][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-14 12:36:05.126][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-14 12:36:05.127][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-14 12:36:05.128][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-14 12:36:05.130][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-14 12:36:05.131][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-14 12:36:05.132][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-14 12:36:05.133][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-14 12:36:05.135][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-14 12:36:05.136][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-14 12:36:05.137][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-14 12:36:05.138][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-14 12:36:05.140][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-14 12:36:05.141][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-14 12:36:05.142][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-14 12:36:05.143][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-14 12:36:05.145][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-14 12:36:05.146][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-14 12:36:05.147][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-14 12:36:05.148][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-14 12:36:05.149][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-14 12:36:05.150][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-14 12:36:05.152][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-14 12:36:05.153][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-14 12:36:05.154][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-14 12:36:05.155][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-14 12:36:05.156][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-14 12:36:05.157][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-14 12:36:05.158][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-14 12:36:05.160][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-14 12:36:05.161][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-14 12:36:05.162][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-14 12:36:05.163][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-14 12:36:05.164][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-14 12:36:05.165][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-14 12:36:05.166][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-14 12:36:05.167][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-14 12:36:05.169][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-14 12:36:05.170][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-14 12:36:05.171][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-14 12:36:05.172][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-14 12:36:05.173][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-14 12:36:05.174][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-14 12:36:05.175][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-14 12:36:05.177][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-14 12:36:05.178][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-14 12:36:05.179][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-14 12:36:05.180][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-14 12:36:05.181][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-14 12:36:05.182][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-14 12:36:05.183][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-14 12:36:05.185][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-14 12:36:05.186][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-14 12:36:05.187][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-14 12:36:05.188][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-14 12:36:05.189][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-14 12:36:05.190][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-14 12:36:05.191][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-14 12:36:05.192][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-14 12:36:05.194][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-14 12:36:05.195][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-14 12:36:05.196][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-14 12:36:05.197][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-14 12:36:05.198][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-14 12:36:05.199][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-14 12:36:05.200][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-14 12:36:05.202][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-14 12:36:05.203][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-14 12:36:05.204][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-14 12:36:05.205][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-14 12:36:05.206][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-14 12:36:05.207][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-14 12:36:05.208][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-14 12:36:05.210][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-14 12:36:05.211][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-14 12:36:05.212][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.213][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:05.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:05.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.219][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[2025-01-14 12:36:05.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:05.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:05.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.224][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[2025-01-14 12:36:05.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:05.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:05.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.229][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[2025-01-14 12:36:05.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:05.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:05.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.234][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[2025-01-14 12:36:05.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:05.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:05.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:05.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:05.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:05.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:05.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:05.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:05.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:05.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:05.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:05.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:05.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:05.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:05.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:05.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:05.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.275][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[2025-01-14 12:36:05.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:05.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:05.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:05.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:05.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:05.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:05.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:05.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:05.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-14 12:36:05.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:05.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:05.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.298][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-01-14 12:36:05.299][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-01-14 12:36:05.301][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:05.301][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-14 12:36:05.302][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:05.303][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-14 12:36:05.310][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:05.310][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-14 12:36:05.310][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:05.311][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-01-14 12:36:05.311][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-14 12:36:05.312][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-14 12:36:05.312][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:05.313][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-01-14 12:36:05.313][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-14 12:36:05.314][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-01-14 12:36:05.314][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-01-14 12:36:05.314][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-01-14 12:36:05.314][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-01-14 12:36:05.314][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-01-14 12:36:05.314][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-01-14 12:36:05.314][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-01-14 12:36:05.314][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-01-14 12:36:05.314][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-01-14 12:36:05.314][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-01-14 12:36:05.314][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-01-14 12:36:05.314][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-14 12:36:05.315][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-14 12:36:05.315][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-14 12:36:05.315][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-14 12:36:05.315][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-14 12:36:05.316][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:05.316][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:05.316][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-14 12:36:05.317][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-14 12:36:05.317][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-14 12:36:05.318][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-14 12:36:05.318][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:36:05.318][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-01-14 12:36:05.318][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-14 12:36:05.319][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-14 12:36:05.320][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-14 12:36:05.320][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-01-14 12:36:05.320][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-01-14 12:36:05.322][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-14 12:36:05.323][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-14 12:36:05.325][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-01-14 12:36:05.326][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-14 12:36:05.327][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-14 12:36:05.328][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-14 12:36:05.331][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-01-14 12:36:05.332][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-01-14 12:36:05.333][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-01-14 12:36:05.334][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-01-14 12:36:05.335][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-14 12:36:05.335][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-14 12:36:05.336][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-01-14 12:36:05.337][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-01-14 12:36:05.338][biodb::testThat]
biodb.INFO [2025-01-14 12:36:05.338][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-01-14 12:36:05.339][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-14 12:36:05.339][biodb::testThat]
biodb.DEBUG[2025-01-14 12:36:05.342][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-01-14 12:36:05.345][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:36:05.346][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-01-14 12:36:05.347][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:36:05.349][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-01-14 12:36:05.352][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[2025-01-14 12:36:05.356][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-14 12:36:05.357][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-01-14 12:36:05.358][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-14 12:36:05.359][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-01-14 12:36:05.364][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-01-14 12:36:05.365][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-14 12:36:05.366][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-01-14 12:36:05.368][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-14 12:36:05.369][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-14 12:36:05.370][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-14 12:36:05.370][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-14 12:36:05.371][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-14 12:36:05.372][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-14 12:36:05.375][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:05.376][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:05.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:05.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-14 12:36:05.385][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-01-14 12:36:05.388][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-14 12:36:05.389][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-14 12:36:05.390][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-01-14 12:36:05.489][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-01-14 12:36:05.627][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-14 12:36:05.630][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-01-14 12:36:05.634][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-01-14 12:36:05.637][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-01-14 12:36:05.639][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-14 12:36:05.640][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-14 12:36:05.641][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-14 12:36:05.643][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-14 12:36:05.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:05.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:05.650][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.651][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-14 12:36:05.657][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:05.658][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:05.659][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.659][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:05.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:05.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.664][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:36:05.665][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:36:05.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.666][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.668][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-14 12:36:05.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-14 12:36:05.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.671][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:36:05.672][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:36:05.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.673][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.675][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-14 12:36:05.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-14 12:36:05.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.678][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-14 12:36:05.679][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-14 12:36:05.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.680][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.682][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-14 12:36:05.682][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-14 12:36:05.683][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.684][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.685][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:36:05.686][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:36:05.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.688][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.689][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:36:05.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-14 12:36:05.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.693][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:36:05.694][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:05.695][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.696][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.697][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-14 12:36:05.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-14 12:36:05.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.700][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:05.701][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:05.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.703][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:05.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-14 12:36:05.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.707][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:36:05.708][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:36:05.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.710][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.711][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-14 12:36:05.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-14 12:36:05.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.715][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:36:05.716][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:36:05.716][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.717][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.718][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-14 12:36:05.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-14 12:36:05.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.722][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:36:05.723][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:36:05.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.724][ef$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.726][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-14 12:36:05.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-14 12:36:05.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.729][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:05.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:05.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.732][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:05.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:05.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:05.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:05.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-14 12:36:05.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-14 12:36:05.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:05.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:05.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:05.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:05.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:05.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:05.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:05.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:05.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:05.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:05.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-14 12:36:05.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-14 12:36:05.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-14 12:36:05.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-14 12:36:05.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-14 12:36:05.761][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-01-14 12:36:05.765][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-14 12:36:05.767][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-01-14 12:36:05.768][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-01-14 12:36:05.768][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-14 12:36:05.769][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-14 12:36:05.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-14 12:36:05.770][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-14 12:36:05.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-14 12:36:05.772][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-14 12:36:05.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 385 ]
> 
> proc.time()
   user  system elapsed 
 17.221   1.054  25.622

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn2.6881.1445.149
ChebiEntry0.4100.0170.430