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This page was generated on 2025-02-03 12:07 -0500 (Mon, 03 Feb 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" 4494
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" 4400
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: 2025-01-30 13:00 -0500 (Thu, 30 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    OK  

CHECK results for biodbChebi on merida1

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: 2025-01-31 00:47:30 -0500 (Fri, 31 Jan 2025)
EndedAt: 2025-01-31 00:50:58 -0500 (Fri, 31 Jan 2025)
EllapsedTime: 207.5 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: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.12.0’
* 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 4.716  1.254   6.908
* 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-x86_64/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: x86_64-apple-darwin20

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

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

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

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2025-01-31 00:49:03.162][biodb::testContext]
biodb.INFO [2025-01-31 00:49:03.170][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-31 00:49:03.173][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-01-31 00:49:03.176][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-31 00:49:03.178][biodb::testContext]
biodb.INFO [2025-01-31 00:49:03.193][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-31 00:49:03.198][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-01-31 00:49:03.213][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-31 00:49:03.216][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-31 00:49:03.218][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-31 00:49:03.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:03.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:03.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:03.230][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-31 00:49:03.304][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-31 00:49:03.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:03.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:03.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:03.313][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-31 00:49:03.315][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-31 00:49:03.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:03.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:03.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:03.324][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-31 00:49:03.326][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-31 00:49:03.328][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-31 00:49:03.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:03.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:03.333][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[2025-01-31 00:49:03.336][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-31 00:49:03.338][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-31 00:49:03.340][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-31 00:49:03.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:03.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:03.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:03.348][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-31 00:49:03.350][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-31 00:49:03.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:03.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:03.356][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[2025-01-31 00:49:03.358][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-31 00:49:03.360][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-31 00:49:03.363][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-31 00:49:03.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:03.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:03.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:03.371][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-31 00:49:03.374][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-31 00:49:03.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:03.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:03.381][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[2025-01-31 00:49:03.384][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-31 00:49:03.387][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-31 00:49:03.389][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-31 00:49:03.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:03.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:03.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:03.398][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-31 00:49:03.400][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-31 00:49:03.403][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-31 00:49:03.405][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-31 00:49:03.408][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-31 00:49:03.410][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-31 00:49:03.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:03.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:03.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:03.419][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-31 00:49:03.421][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-31 00:49:03.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:03.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:03.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:03.429][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-31 00:49:03.432][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-31 00:49:03.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:03.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:03.438][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.DEBUG[2025-01-31 00:49:03.441][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-31 00:49:03.443][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-31 00:49:03.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:03.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:03.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:03.452][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-31 00:49:03.455][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-31 00:49:03.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:03.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:03.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:03.464][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-31 00:49:03.466][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-31 00:49:03.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:03.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:03.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:03.475][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-31 00:49:03.477][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-31 00:49:03.500][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-31 00:49:03.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:03.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:03.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:03.510][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-31 00:49:03.512][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-31 00:49:03.515][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-31 00:49:03.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:03.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:03.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:03.528][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-31 00:49:03.615][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-31 00:49:03.659][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-31 00:49:03.662][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-31 00:49:03.665][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-31 00:49:03.667][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-31 00:49:03.670][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-31 00:49:03.672][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-31 00:49:03.675][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-31 00:49:03.677][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-31 00:49:03.679][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-31 00:49:03.682][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-31 00:49:03.685][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-31 00:49:03.687][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-31 00:49:03.690][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:49:03.692][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-31 00:49:03.695][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-31 00:49:03.695][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-31 00:49:03.695][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-31 00:49:03.695][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-31 00:49:03.695][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-31 00:49:03.698][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-31 00:49:03.700][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:49:03.702][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:49:03.705][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-31 00:49:03.707][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:49:03.710][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:49:03.713][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-31 00:49:03.715][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:49:03.727][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-31 00:49:03.729][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-31 00:49:03.731][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-31 00:49:03.734][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:49:03.737][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-31 00:49:03.741][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-31 00:49:03.744][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-31 00:49:03.746][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-31 00:49:03.749][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-31 00:49:03.752][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-31 00:49:03.755][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-31 00:49:03.757][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-31 00:49:03.760][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-31 00:49:03.762][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-31 00:49:03.765][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-31 00:49:03.767][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-31 00:49:03.770][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-31 00:49:03.772][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-31 00:49:03.774][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:49:03.776][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-31 00:49:03.779][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-31 00:49:03.779][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-31 00:49:03.779][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-31 00:49:03.779][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-31 00:49:03.779][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-31 00:49:03.781][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-31 00:49:03.783][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:49:03.785][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:49:03.787][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-31 00:49:03.789][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:49:03.791][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:49:03.793][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-31 00:49:03.795][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:49:03.797][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-31 00:49:03.799][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-31 00:49:03.801][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-31 00:49:03.804][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:49:03.806][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-31 00:49:03.810][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-31 00:49:03.813][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-31 00:49:03.816][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-31 00:49:03.818][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-31 00:49:03.820][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-31 00:49:03.822][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-31 00:49:03.825][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-31 00:49:03.827][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-31 00:49:03.830][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-31 00:49:03.832][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-31 00:49:03.835][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-31 00:49:03.837][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-31 00:49:03.840][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-31 00:49:03.842][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:49:03.844][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-31 00:49:03.846][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:49:03.849][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-31 00:49:03.851][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:49:03.853][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:49:03.856][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-31 00:49:03.858][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:49:03.860][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:49:03.862][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-31 00:49:03.864][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:49:03.867][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-31 00:49:03.868][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-31 00:49:03.870][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-31 00:49:03.873][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:49:03.876][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-31 00:49:03.880][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-31 00:49:03.882][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-31 00:49:03.885][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-31 00:49:03.887][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-31 00:49:03.890][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-31 00:49:03.892][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-31 00:49:03.895][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-31 00:49:03.897][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-31 00:49:03.899][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-31 00:49:03.902][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-31 00:49:03.905][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-31 00:49:03.907][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-31 00:49:03.909][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-31 00:49:03.912][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:49:03.914][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-31 00:49:03.917][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:49:03.919][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-31 00:49:03.921][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:49:03.924][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:49:03.927][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-31 00:49:03.929][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:49:03.931][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:49:03.934][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-31 00:49:03.936][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:49:03.939][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-31 00:49:03.941][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-31 00:49:03.943][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-31 00:49:03.945][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:49:03.953][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-31 00:49:03.955][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:03.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:03.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:03.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:03.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:03.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:03.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:03.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:03.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:03.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:03.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:03.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:03.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:03.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:03.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:03.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:03.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:03.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:03.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:03.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:04.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:04.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.023][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.DEBUG[2025-01-31 00:49:04.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:04.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:04.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.059][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[2025-01-31 00:49:04.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:04.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:04.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.093][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[2025-01-31 00:49:04.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.104][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[2025-01-31 00:49:04.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.116][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[2025-01-31 00:49:04.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.127][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[2025-01-31 00:49:04.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:04.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.152][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.DEBUG[2025-01-31 00:49:04.154][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-31 00:49:04.172][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-31 00:49:04.175][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-31 00:49:04.179][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-31 00:49:04.183][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-31 00:49:04.186][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-31 00:49:04.190][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-31 00:49:04.193][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-31 00:49:04.196][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-31 00:49:04.199][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-31 00:49:04.202][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-31 00:49:04.206][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-31 00:49:04.209][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-31 00:49:04.212][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-31 00:49:04.216][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-31 00:49:04.219][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-31 00:49:04.222][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-31 00:49:04.225][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-31 00:49:04.229][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-31 00:49:04.232][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-31 00:49:04.236][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-31 00:49:04.240][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-31 00:49:04.244][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-31 00:49:04.248][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-31 00:49:04.251][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-31 00:49:04.255][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-31 00:49:04.258][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-31 00:49:04.261][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-31 00:49:04.265][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-31 00:49:04.268][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-31 00:49:04.272][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-31 00:49:04.276][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-31 00:49:04.279][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-31 00:49:04.282][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-31 00:49:04.286][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-31 00:49:04.289][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-31 00:49:04.293][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-31 00:49:04.296][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-31 00:49:04.300][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-31 00:49:04.303][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-31 00:49:04.307][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-31 00:49:04.310][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-31 00:49:04.314][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-31 00:49:04.318][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-31 00:49:04.321][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-31 00:49:04.325][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-31 00:49:04.329][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-31 00:49:04.332][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-31 00:49:04.336][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-31 00:49:04.340][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-31 00:49:04.343][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-31 00:49:04.347][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-31 00:49:04.350][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-31 00:49:04.354][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-31 00:49:04.357][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-31 00:49:04.361][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-31 00:49:04.364][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-31 00:49:04.368][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-31 00:49:04.371][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-31 00:49:04.375][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-31 00:49:04.379][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-31 00:49:04.382][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-31 00:49:04.385][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-31 00:49:04.389][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-31 00:49:04.392][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-31 00:49:04.395][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-31 00:49:04.399][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-31 00:49:04.402][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-31 00:49:04.406][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-31 00:49:04.409][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-31 00:49:04.413][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-31 00:49:04.417][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-31 00:49:04.421][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-31 00:49:04.424][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-31 00:49:04.428][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-31 00:49:04.431][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-31 00:49:04.434][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-31 00:49:04.438][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-31 00:49:04.441][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-31 00:49:04.444][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-31 00:49:04.448][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-31 00:49:04.451][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-31 00:49:04.454][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-31 00:49:04.470][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-31 00:49:04.474][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-31 00:49:04.480][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-31 00:49:04.483][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.487][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.489][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[2025-01-31 00:49:04.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:04.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:04.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:04.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:04.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:04.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:04.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:04.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:04.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:04.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:04.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:04.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.557][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.DEBUG[2025-01-31 00:49:04.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:04.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:04.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.574][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[2025-01-31 00:49:04.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:04.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:04.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:04.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:04.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:04.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:04.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:04.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:04.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:04.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:04.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:04.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:04.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:04.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:04.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.657][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[2025-01-31 00:49:04.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:04.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:04.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:04.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:04.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:04.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:04.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:04.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:04.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:04.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:04.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:04.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:04.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:04.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:04.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:04.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:04.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:04.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:04.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:49:04.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:04.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:04.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:04.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:04.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:04.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:04.789][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-01-31 00:49:04.814][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-01-31 00:49:04.818][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-31 00:49:04.821][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-31 00:49:04.823][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-31 00:49:04.825][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-31 00:49:04.827][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-31 00:49:04.830][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-31 00:49:04.832][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-31 00:49:04.834][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-01-31 00:49:04.837][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-31 00:49:04.839][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-31 00:49:04.842][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-31 00:49:04.844][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-01-31 00:49:04.846][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-31 00:49:04.849][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-01-31 00:49:04.849][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-01-31 00:49:04.849][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-01-31 00:49:04.849][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-01-31 00:49:04.849][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-01-31 00:49:04.849][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-01-31 00:49:04.849][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-01-31 00:49:04.849][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-01-31 00:49:04.849][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-01-31 00:49:04.849][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-01-31 00:49:04.849][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-01-31 00:49:04.851][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-31 00:49:04.853][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-31 00:49:04.853][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-31 00:49:04.853][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-31 00:49:04.856][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-31 00:49:04.858][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:49:04.860][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:49:04.862][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-31 00:49:04.865][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:49:04.867][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:49:04.869][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-31 00:49:04.871][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:04.871][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-01-31 00:49:04.874][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-31 00:49:04.876][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-31 00:49:04.878][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-31 00:49:04.880][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-01-31 00:49:04.880][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-01-31 00:49:04.895][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-31 00:49:04.898][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-31 00:49:04.902][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-01-31 00:49:04.905][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-31 00:49:04.909][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-31 00:49:04.913][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-31 00:49:04.956][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-01-31 00:49:04.958][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-01-31 00:49:04.967][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-01-31 00:49:04.976][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-01-31 00:49:04.984][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-31 00:49:04.986][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-31 00:49:04.988][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-01-31 00:49:04.990][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-01-31 00:49:05.009][biodb::testThat]
biodb.INFO [2025-01-31 00:49:05.011][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-01-31 00:49:05.013][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:49:05.015][biodb::testThat]
biodb.TRACE[2025-01-31 00:49:05.022][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-01-31 00:49:05.026][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:05.043][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:05.059][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:05.061][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:05.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:05.090][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:05.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:05.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:05.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:05.113][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:05.115][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:05.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.119][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:05.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:05.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.163][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:05.166][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:05.168][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.170][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.240][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:05.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:05.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.249][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:05.251][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:05.253][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.255][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.258][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:05.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:05.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.266][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:05.268][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:05.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.272][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.275][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:05.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:05.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.285][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:05.287][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:05.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.291][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.294][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:05.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:05.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.303][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:05.306][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:05.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.310][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.313][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:05.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:05.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.322][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:05.324][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:05.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.328][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.331][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:05.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:05.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.341][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:05.344][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:05.346][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.348][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:05.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:05.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.360][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:05.363][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:05.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.367][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.370][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:05.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:05.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.379][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:05.381][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:05.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.385][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.432][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:05.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:05.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.441][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:05.443][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:05.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.448][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.450][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:05.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:05.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:05.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:05.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:05.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:05.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:05.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:05.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:05.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:05.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:05.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:05.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:05.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:05.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:05.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:05.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:05.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:05.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:05.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:05.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:05.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:05.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:05.637][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-01-31 00:49:05.642][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:05.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:05.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.651][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:05.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:05.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.721][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:05.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:05.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.731][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:05.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:05.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.748][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:05.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:05.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.757][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:05.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:05.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.767][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-31 00:49:05.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-31 00:49:05.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.776][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-31 00:49:05.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-31 00:49:05.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.785][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-31 00:49:05.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-31 00:49:05.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.795][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-31 00:49:05.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-31 00:49:05.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:05.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:05.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:05.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:05.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:05.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:05.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:05.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:05.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:05.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:05.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:05.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:05.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:05.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:05.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:05.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:05.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:05.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:05.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:05.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:05.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:05.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:05.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:05.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:05.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:06.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:06.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:06.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:06.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:06.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:06.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.025][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:06.028][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:06.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.032][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:06.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:06.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:06.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:06.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:06.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:06.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:06.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:06.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.099][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:06.102][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:06.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.107][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:06.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:06.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.138][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:06.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:06.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.148][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:06.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:06.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.157][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:06.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:06.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.167][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:06.170][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:06.172][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.174][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.177][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:06.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:06.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.206][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:06.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:06.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.216][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:06.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:06.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.225][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:06.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:06.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.235][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:06.237][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:06.239][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.242][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.244][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:06.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:06.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.271][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:06.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:06.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.281][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:06.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:06.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:06.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:06.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.300][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:06.303][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:06.305][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.308][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.310][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:06.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:06.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:06.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:06.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:06.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:06.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:06.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:06.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.368][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:06.371][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:06.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.375][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:06.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:06.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.406][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:06.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:06.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.416][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:06.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:06.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.422][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:06.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:06.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.433][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:06.434][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:06.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.437][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.438][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:06.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:06.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.467][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-31 00:49:06.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:06.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.477][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-31 00:49:06.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:06.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.487][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-31 00:49:06.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:06.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.496][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-31 00:49:06.498][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:06.501][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.503][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.505][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-31 00:49:06.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:06.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.534][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:06.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:06.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.544][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:06.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:06.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.555][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:06.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:06.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.565][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:06.568][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:06.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.574][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.576][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:06.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:06.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.606][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:06.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:06.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.615][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:06.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:06.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.623][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:06.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:06.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.632][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:06.634][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:06.637][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.639][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.641][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:06.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:06.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.669][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:06.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:06.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.678][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:06.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:06.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.687][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:06.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:06.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.695][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:06.698][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:06.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.702][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.704][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:06.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:06.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.733][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:06.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:06.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:06.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:06.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.752][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:06.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:06.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.769][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:06.771][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:06.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.776][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.778][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:06.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:06.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.803][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:06.806][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:06.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.809][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.820][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:06.823][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:06.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.827][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.838][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:06.841][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:06.843][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.845][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.856][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:06.858][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:06.860][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.863][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.874][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:06.876][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:06.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.880][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.891][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:06.894][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:06.896][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.898][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.910][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:06.913][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:06.915][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.917][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.928][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:06.931][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:06.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.935][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.947][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-31 00:49:06.949][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:06.952][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.954][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.965][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:06.968][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:06.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.972][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:06.983][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:06.986][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:06.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:06.990][ef$get] fields variable is a list.
biodb.INFO [2025-01-31 00:49:07.009][biodb::testThat]
biodb.INFO [2025-01-31 00:49:07.011][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-01-31 00:49:07.013][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:49:07.016][biodb::testThat]
biodb.DEBUG[2025-01-31 00:49:07.052][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-01-31 00:49:07.066][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:07.074][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-01-31 00:49:07.078][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-31 00:49:07.081][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-01-31 00:49:07.083][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:07.151][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:07.154][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:07.158][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:07.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:07.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:07.173][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:07.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:07.178][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:07.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:07.185][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:07.188][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:07.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.193][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:07.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:07.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.250][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:07.253][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:07.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.257][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.331][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:07.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:07.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.343][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:07.345][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:07.348][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.350][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.353][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:07.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:07.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.363][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:07.366][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:07.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.370][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.373][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:07.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:07.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.382][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:07.385][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:07.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.389][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.392][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:07.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:07.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.401][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:07.404][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:07.406][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.408][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.419][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:07.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:07.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.429][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:07.431][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:07.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.436][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.438][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:07.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:07.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.447][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:07.449][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:07.452][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.454][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.457][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:07.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:07.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.466][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:07.469][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:07.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.473][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.476][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:07.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:07.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.486][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:07.489][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:07.491][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.493][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.496][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:07.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:07.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.506][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:07.508][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:07.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.512][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.515][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:07.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:07.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:07.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:07.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:07.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:07.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:07.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:07.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:07.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:07.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:07.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:07.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:07.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:07.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:07.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:07.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:07.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:07.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:07.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:07.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:07.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:07.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:07.710][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-01-31 00:49:07.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-01-31 00:49:07.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-01-31 00:49:07.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-01-31 00:49:07.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-01-31 00:49:07.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.737][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-01-31 00:49:07.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-01-31 00:49:07.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-31 00:49:07.763][biodb::testThat]
biodb.INFO [2025-01-31 00:49:07.765][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-01-31 00:49:07.767][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:49:07.770][biodb::testThat]
biodb.TRACE[2025-01-31 00:49:07.776][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:07.779][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:07.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.783][ef$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:07.786][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-01-31 00:49:07.852][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:07.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:07.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.862][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:07.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:07.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:07.871][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:07.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:07.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:07.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:07.887][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-01-31 00:49:07.896][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-01-31 00:49:07.948][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-31 00:49:07.991][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-01-31 00:49:07.994][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-31 00:49:07.997][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-01-31 00:49:08.067][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:49:08.075][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:08.078][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:08.082][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-01-31 00:49:08.929][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-01-31 00:49:09.543][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:09.549][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-01-31 00:49:09.590][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-01-31 00:49:09.596][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-01-31 00:49:09.625][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:09.628][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:09.630][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:09.633][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:09.635][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:09.638][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:09.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:09.642][ef$get] fields variable is a list.
biodb.INFO [2025-01-31 00:49:09.652][biodb::testThat]
biodb.INFO [2025-01-31 00:49:09.654][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-01-31 00:49:09.657][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:49:09.659][biodb::testThat]
biodb.TRACE[2025-01-31 00:49:09.722][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:09.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:09.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:09.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:09.732][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:09.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:09.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:09.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:09.742][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:09.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:09.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:09.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:09.912][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:49:09.919][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-31 00:49:09.923][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-31 00:49:09.926][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-31 00:49:09.930][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-01-31 00:49:09.971][biodb::testThat]
biodb.INFO [2025-01-31 00:49:09.973][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-01-31 00:49:09.975][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:49:09.977][biodb::testThat]
biodb.TRACE[2025-01-31 00:49:10.030][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:10.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:10.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:10.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:10.039][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:10.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:10.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:10.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:10.057][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:10.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:10.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:10.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:10.067][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:10.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:10.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:10.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:10.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:10.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:10.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:10.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:10.086][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:10.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:10.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:10.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:10.095][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-31 00:49:10.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-31 00:49:10.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:10.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:10.104][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-31 00:49:10.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-31 00:49:10.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:10.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:10.113][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-31 00:49:10.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-31 00:49:10.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:10.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:10.123][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-31 00:49:10.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-31 00:49:10.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:10.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:10.179][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:10.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:10.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:10.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:10.188][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:10.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:10.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:10.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:10.199][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:10.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:10.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:10.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:10.208][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:10.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:10.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:10.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:10.217][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:10.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:10.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:10.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:10.226][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:10.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:10.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:10.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:10.236][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-31 00:49:10.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-31 00:49:10.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:10.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:10.245][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-31 00:49:10.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-31 00:49:10.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:10.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:10.255][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-31 00:49:10.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-31 00:49:10.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:10.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:10.264][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-31 00:49:10.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-31 00:49:10.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:10.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-31 00:49:10.287][biodb::testThat]
biodb.INFO [2025-01-31 00:49:10.290][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-01-31 00:49:10.299][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:49:10.301][biodb::testThat]
biodb.INFO [2025-01-31 00:49:10.321][biodb::testThat]
biodb.INFO [2025-01-31 00:49:10.323][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-01-31 00:49:10.325][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:49:10.327][biodb::testThat]
biodb.INFO [2025-01-31 00:49:10.347][biodb::testThat]
biodb.INFO [2025-01-31 00:49:10.350][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-01-31 00:49:10.352][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:49:10.355][biodb::testThat]
biodb.DEBUG[2025-01-31 00:49:10.363][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-01-31 00:49:11.661][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-01-31 00:49:12.990][biodb::testThat]
biodb.INFO [2025-01-31 00:49:12.992][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-01-31 00:49:12.994][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:49:12.997][biodb::testThat]
biodb.DEBUG[2025-01-31 00:49:13.468][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[2025-01-31 00:49:13.932][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:13.934][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:13.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:13.938][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:13.940][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:13.943][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:13.945][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:13.947][ef$get] fields variable is a list.
biodb.INFO [2025-01-31 00:49:13.951][biodb::testThat]
biodb.INFO [2025-01-31 00:49:13.953][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-01-31 00:49:13.955][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:49:13.957][biodb::testThat]
biodb.TRACE[2025-01-31 00:49:13.982][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:13.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:13.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:13.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:13.991][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:13.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:13.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:13.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:14.001][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:14.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:14.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:14.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:14.206][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:49:14.214][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-31 00:49:14.217][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-31 00:49:14.220][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-31 00:49:14.223][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-01-31 00:49:14.389][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:49:14.398][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-31 00:49:14.401][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-31 00:49:14.404][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-31 00:49:14.408][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-01-31 00:49:14.441][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-31 00:49:14.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-31 00:49:14.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:14.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:14.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:14.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:14.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:14.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:14.472][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:14.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:14.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:14.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:14.483][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:14.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:14.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:14.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:14.492][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:14.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:14.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:14.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:14.501][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:14.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:14.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:14.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:14.524][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:49:14.577][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:14.580][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:14.623][private$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[2025-01-31 00:49:15.022][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[2025-01-31 00:49:15.415][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:15.419][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-01-31 00:49:15.428][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-01-31 00:49:15.434][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:15.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:15.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:15.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:15.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:15.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:15.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:15.458][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-01-31 00:49:15.584][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:15.588][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-01-31 00:49:15.591][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:15.593][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:15.595][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:15.598][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:15.600][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:15.602][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:15.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:15.611][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:15.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:15.623][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:15.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:15.627][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:15.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:15.632][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-01-31 00:49:15.638][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:15.640][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:15.643][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-01-31 00:49:17.061][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-01-31 00:49:17.453][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:17.458][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-01-31 00:49:17.466][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-01-31 00:49:17.471][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-01-31 00:49:17.475][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:17.478][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:17.480][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:17.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:17.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:17.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:17.494][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:17.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:17.499][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:17.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:17.504][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:17.505][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:17.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.509][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:17.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:17.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.521][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:17.536][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:17.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.540][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.595][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:17.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:17.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.605][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:17.607][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:17.609][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.612][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.615][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:17.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:17.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.624][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:17.625][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:17.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.630][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.633][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:17.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:17.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.642][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:17.645][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:17.646][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.648][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.650][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:17.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:17.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.659][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:17.662][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:17.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.667][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.669][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:17.671][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:17.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.675][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.678][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:17.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:17.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.687][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:17.689][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:17.690][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.692][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.695][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:17.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:17.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.705][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:17.707][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:17.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.712][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.720][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:17.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:17.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.727][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:17.730][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:17.732][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.734][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.735][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:17.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:17.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.741][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:17.742][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:17.745][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.747][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.750][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:17.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:17.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:17.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:17.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:17.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:17.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:17.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:17.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.788][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:17.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:17.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:17.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:17.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:17.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:17.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:17.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:17.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:17.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:17.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:17.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:17.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:17.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:17.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:17.947][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-01-31 00:49:17.971][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:17.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:17.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.980][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:17.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:17.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:17.989][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:17.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:17.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:17.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:18.001][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[2025-01-31 00:49:18.009][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:18.011][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:18.016][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-01-31 00:49:18.413][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-01-31 00:49:18.822][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:18.826][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-01-31 00:49:18.835][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-01-31 00:49:18.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:18.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:18.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:18.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:18.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:18.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:18.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:18.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:18.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:18.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:18.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:18.909][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:18.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:18.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:18.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:18.923][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:18.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:18.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:18.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:18.932][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:18.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:18.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:18.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:18.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:18.952][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:18.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:18.956][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-01-31 00:49:18.957][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:18.960][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-01-31 00:49:18.963][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:18.965][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:18.968][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:18.970][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:18.972][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:18.974][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:19.025][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:19.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:19.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:19.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:19.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:19.043][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:19.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:19.047][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-01-31 00:49:19.052][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:19.054][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:19.058][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-01-31 00:49:19.472][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-01-31 00:49:19.869][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:19.874][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-01-31 00:49:19.883][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-01-31 00:49:19.889][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-01-31 00:49:19.893][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:19.896][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:19.899][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:19.903][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:19.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:19.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:19.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:19.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:19.922][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:19.924][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.TRACE[2025-01-31 00:49:19.928][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:19.930][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:19.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:19.934][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:19.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:19.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:19.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:19.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:19.983][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:19.986][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:19.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:19.990][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.061][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:20.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:20.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.071][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:20.074][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:20.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.078][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.081][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:20.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:20.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.090][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:20.092][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:20.094][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.096][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.099][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:20.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:20.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.107][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:20.110][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:20.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.113][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.115][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:20.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:20.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.125][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:20.127][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:20.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.131][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.133][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:20.135][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:20.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.138][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.141][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:20.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:20.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.150][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:20.152][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:20.154][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.156][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:20.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:20.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.168][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:20.177][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:20.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.182][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.185][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:20.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:20.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.194][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:20.197][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:20.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.201][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.204][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:20.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:20.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.213][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:20.216][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:20.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.220][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.223][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:20.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:20.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.232][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:20.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:20.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:20.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:20.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:20.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:20.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.259][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:20.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:20.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:20.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:20.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:20.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:20.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:20.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:20.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:20.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:20.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:20.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:20.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:20.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:20.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:20.403][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-01-31 00:49:20.404][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:20.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:20.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.412][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:20.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:20.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:20.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:20.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:20.472][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:49:20.480][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-31 00:49:20.483][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-31 00:49:20.486][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-31 00:49:20.489][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-01-31 00:49:20.496][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:20.498][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:20.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:20.509][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:20.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:20.513][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:20.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:20.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:20.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:20.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.525][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:20.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:20.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:20.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:20.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:20.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:20.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:20.540][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:20.541][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:20.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:20.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:20.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:20.559][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:20.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:20.564][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-01-31 00:49:20.567][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:20.571][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-01-31 00:49:20.574][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:20.577][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:20.588][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:20.590][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:20.592][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:20.595][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:20.601][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:20.603][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:20.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:20.613][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:20.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:20.616][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:20.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:20.618][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-01-31 00:49:20.625][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:20.626][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:20.628][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-01-31 00:49:21.047][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-01-31 00:49:21.438][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:21.442][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-01-31 00:49:21.450][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-01-31 00:49:21.456][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-01-31 00:49:21.459][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:21.462][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:21.464][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:21.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:21.470][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:21.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:21.481][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:21.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:21.485][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:21.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:21.491][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:21.493][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:21.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.498][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:21.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:21.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.509][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:21.512][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:21.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.516][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.518][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:21.520][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:21.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.525][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.528][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:21.530][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:21.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.534][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.537][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:21.540][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:21.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.544][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.547][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:21.549][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:21.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.554][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.557][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:21.559][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:21.562][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.564][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.567][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:21.569][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:21.572][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.574][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.577][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:21.579][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:21.581][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.583][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.662][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:21.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:21.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.672][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:21.674][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:21.676][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.679][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.681][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:21.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:21.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.692][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:21.695][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:21.697][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.699][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:21.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:21.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:21.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:21.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:21.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:21.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:21.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:21.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:21.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:21.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:21.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:21.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:21.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:21.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:21.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:21.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:21.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:21.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:21.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:21.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:21.910][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-01-31 00:49:21.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:21.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:21.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:21.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:21.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.930][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:21.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:21.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:21.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:21.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:21.948][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:21.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:21.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:21.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:21.957][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:21.959][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:21.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:21.974][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:21.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:21.979][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:21.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:21.983][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-01-31 00:49:21.986][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:21.990][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-01-31 00:49:21.993][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:21.995][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:21.998][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:22.000][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:22.002][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:22.004][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:22.010][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:22.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:22.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:22.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:22.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:22.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:22.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:22.043][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-01-31 00:49:22.049][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:22.052][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:22.055][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-01-31 00:49:22.483][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-01-31 00:49:22.884][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:22.888][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-01-31 00:49:22.897][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-01-31 00:49:22.903][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-01-31 00:49:22.907][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:22.910][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:22.913][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:22.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:22.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:22.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:22.932][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:22.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:22.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:22.938][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.TRACE[2025-01-31 00:49:22.943][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:22.946][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:22.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:22.950][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:22.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:22.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:22.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:22.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:22.961][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:22.963][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:22.965][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:22.967][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:22.969][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:22.971][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:22.972][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:22.974][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:22.977][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:22.979][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:22.980][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:22.982][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:22.985][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:22.986][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:22.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:22.989][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:22.990][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:22.992][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:22.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:22.997][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:23.000][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:23.002][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:23.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:23.007][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:23.010][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:23.013][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:23.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:23.018][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:23.021][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:23.024][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:23.026][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:23.029][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:23.117][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:23.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:23.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:23.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:23.125][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:23.127][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:23.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:23.132][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:23.134][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:23.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:23.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:23.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:23.144][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:23.146][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:23.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:23.151][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:23.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:23.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:23.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:23.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:23.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:23.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:23.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:23.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:23.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:23.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:23.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:23.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:23.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:23.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:23.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:23.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:23.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:23.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:23.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:23.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:23.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:23.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:23.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:23.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:23.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:23.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:23.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:23.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:23.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:23.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:23.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:23.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:23.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:23.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:23.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:23.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:23.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:23.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:23.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:23.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:23.343][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-01-31 00:49:23.346][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:23.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:23.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:23.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:23.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:23.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:23.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:23.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:23.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:23.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:23.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:23.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:23.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:23.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:23.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:23.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:23.384][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:23.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:23.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:23.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:23.394][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:23.396][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:23.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:23.408][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:23.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:23.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:23.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:23.417][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-01-31 00:49:23.420][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:23.424][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-01-31 00:49:23.427][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:23.429][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:23.432][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:23.435][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:23.437][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:23.439][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:23.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:23.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:23.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:23.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:23.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:23.465][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:23.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:23.470][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-01-31 00:49:23.476][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:23.478][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:23.481][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-01-31 00:49:23.894][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-01-31 00:49:24.285][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:24.303][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-01-31 00:49:24.312][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-01-31 00:49:24.318][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-01-31 00:49:24.355][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:24.358][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:24.360][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:24.364][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:24.366][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:24.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:24.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:24.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:24.385][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:24.387][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[2025-01-31 00:49:24.392][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:24.395][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:24.397][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.399][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:24.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:24.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.412][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:24.414][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:24.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.419][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.422][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:24.424][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:24.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.429][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.432][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:24.435][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:24.437][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.439][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.441][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:24.444][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:24.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.449][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.452][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:24.454][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:24.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.459][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.462][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:24.465][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:24.467][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.470][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.472][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:24.474][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:24.477][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.479][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.482][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:24.484][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:24.487][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.489][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.568][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:24.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:24.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.577][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:24.580][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:24.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.584][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.586][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:24.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:24.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.595][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:24.597][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:24.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.601][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:24.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:24.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:24.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:24.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:24.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:24.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:24.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:24.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:24.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:24.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:24.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:24.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:24.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:24.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:24.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:24.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:24.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:24.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:24.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:24.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:24.792][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-01-31 00:49:24.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:24.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:24.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.804][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:24.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:24.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.814][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:24.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:24.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:24.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:24.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:24.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:24.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:24.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:24.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:24.842][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:24.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:24.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:24.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:24.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:24.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:24.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:24.866][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-01-31 00:49:24.869][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:24.873][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-01-31 00:49:24.876][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:24.878][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:24.880][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:24.882][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:24.885][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:24.887][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:24.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:24.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:24.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:24.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:24.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:24.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:24.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:24.917][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-01-31 00:49:24.924][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:24.927][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:24.930][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-01-31 00:49:25.570][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-01-31 00:49:25.985][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:25.990][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-01-31 00:49:25.998][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-01-31 00:49:26.004][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-01-31 00:49:26.049][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:26.052][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:26.062][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:26.070][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:26.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:26.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:26.085][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:26.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:26.089][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:26.090][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.TRACE[2025-01-31 00:49:26.095][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:26.098][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:26.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.102][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:26.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:26.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.114][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:26.116][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:26.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.120][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.188][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:26.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:26.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.198][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:26.200][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:26.202][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.204][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.208][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:26.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:26.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.217][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:26.220][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:26.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.224][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.226][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:26.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:26.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.234][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:26.236][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:26.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.240][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:26.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:26.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.249][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:26.252][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:26.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.263][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.266][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:26.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:26.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.276][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:26.277][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:26.279][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.282][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.285][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:26.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:26.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.293][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:26.295][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:26.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.299][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:26.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:26.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.310][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:26.312][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:26.315][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.317][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.321][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:26.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:26.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.328][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:26.329][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:26.331][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.333][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.335][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:26.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:26.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.344][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:26.347][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:26.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.351][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.354][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:26.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:26.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:26.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:26.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:26.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:26.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:26.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:26.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:26.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:26.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:26.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:26.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:26.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:26.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:26.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:26.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:26.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:26.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:26.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:26.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:26.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:26.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:26.556][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-01-31 00:49:26.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:26.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:26.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:26.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:26.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:26.577][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:26.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:26.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:26.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:26.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:26.588][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:26.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:26.601][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:26.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:26.605][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:26.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:26.610][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-01-31 00:49:26.613][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:26.616][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-01-31 00:49:26.620][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:26.622][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:26.625][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:26.627][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:26.629][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:26.631][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:26.637][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:26.640][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:26.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:26.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:26.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:26.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:26.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:26.663][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-01-31 00:49:26.678][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:26.681][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:26.685][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-01-31 00:49:27.144][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-01-31 00:49:27.557][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:27.562][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-01-31 00:49:27.570][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-01-31 00:49:27.576][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-01-31 00:49:27.580][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:27.583][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:27.586][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:27.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:27.591][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:27.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:27.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:27.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:27.608][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:27.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:27.615][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:27.617][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:27.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.622][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:27.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:27.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.634][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:27.637][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:27.639][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.641][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.711][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:27.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:27.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.720][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:27.722][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:27.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.727][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.730][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:27.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:27.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.739][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:27.742][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:27.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.745][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.761][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:27.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:27.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.772][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:27.775][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:27.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.779][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.782][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:27.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:27.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.792][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:27.795][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:27.797][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.799][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.802][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:27.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:27.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.812][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:27.815][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:27.817][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.819][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.822][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:27.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:27.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.831][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:27.834][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:27.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.838][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:27.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:27.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.851][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:27.854][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:27.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.857][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.860][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:27.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:27.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.869][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:27.872][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:27.874][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.876][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.879][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:27.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:27.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.888][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:27.891][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:27.893][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.895][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.898][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:27.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:27.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:27.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:27.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:27.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:27.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:27.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:27.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:27.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:27.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:27.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:27.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:27.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:27.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:27.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:27.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:27.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:27.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:28.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:28.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:28.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:28.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:28.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:28.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:28.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:28.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:28.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:28.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:28.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:28.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:28.098][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-01-31 00:49:28.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:28.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:28.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:28.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:28.109][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:28.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:28.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:28.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:28.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:28.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:28.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:28.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:28.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:28.130][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:28.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:28.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:28.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:28.147][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:28.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:28.152][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-01-31 00:49:28.155][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:28.159][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-01-31 00:49:28.162][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:28.165][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:28.169][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:28.172][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:28.174][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:28.177][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:28.183][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:28.193][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:28.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:28.208][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:28.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:28.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:28.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:28.217][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-01-31 00:49:28.224][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:28.226][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:28.228][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-01-31 00:49:28.646][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-01-31 00:49:29.048][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:29.053][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-01-31 00:49:29.061][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-01-31 00:49:29.067][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-01-31 00:49:29.071][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:29.073][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:29.075][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:29.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:29.081][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:29.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:29.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:29.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:29.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:29.099][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[2025-01-31 00:49:29.104][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:29.106][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:29.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.111][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:29.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:29.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.122][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:29.124][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:29.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.128][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.200][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:29.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:29.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.222][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:29.225][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:29.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.230][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.233][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:29.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:29.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.243][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:29.246][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:29.248][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.250][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.253][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:29.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:29.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.263][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:29.265][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:29.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.270][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.272][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:29.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:29.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.281][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:29.283][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:29.285][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.287][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.290][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:29.292][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:29.295][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.297][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.300][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:29.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:29.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.309][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:29.311][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:29.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.316][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:29.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:29.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.328][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:29.330][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:29.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.335][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.338][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:29.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:29.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.348][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:29.350][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:29.353][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.354][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.358][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:29.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:29.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.368][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:29.370][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:29.372][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.374][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.377][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:29.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:29.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:29.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:29.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:29.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:29.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:29.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:29.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.413][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:29.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:29.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:29.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:29.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:29.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:29.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:29.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:29.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:29.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:29.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:29.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:29.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:29.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:29.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:29.563][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-01-31 00:49:29.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:29.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:29.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:29.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:29.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:29.581][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:29.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:29.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:29.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:29.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:29.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:29.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:29.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:29.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:29.611][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:29.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:29.615][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-01-31 00:49:29.617][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:29.621][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-01-31 00:49:29.631][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:29.634][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:29.636][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:29.638][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:29.641][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:29.643][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:29.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:29.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:29.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:29.665][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:29.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:29.669][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:29.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:29.674][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-01-31 00:49:29.681][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:29.684][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:29.687][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-01-31 00:49:30.113][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-01-31 00:49:30.517][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:30.522][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-01-31 00:49:30.531][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-01-31 00:49:30.537][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-01-31 00:49:30.541][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:30.543][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:30.546][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:30.549][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:30.551][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:30.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:30.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:30.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:30.613][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:30.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:30.620][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:30.624][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:30.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:30.628][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:30.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:30.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:30.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:30.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:30.639][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:30.642][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:30.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:30.647][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:30.900][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:30.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:30.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:30.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:30.909][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:30.912][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:30.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:30.916][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:30.918][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:30.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:30.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:30.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:30.928][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:30.930][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:30.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:30.934][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:30.937][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:30.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:30.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:30.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:30.946][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:30.948][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:30.950][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:30.952][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:30.955][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:30.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:30.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:30.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:30.982][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:30.985][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:30.987][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:30.989][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:30.991][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:30.994][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:30.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:30.999][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:31.001][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:31.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:31.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:31.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:31.011][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:31.013][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:31.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:31.018][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:31.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:31.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:31.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:31.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:31.030][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:31.033][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:31.034][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:31.036][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:31.039][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:31.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:31.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:31.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:31.049][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:31.052][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:31.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:31.056][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:31.059][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:31.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:31.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:31.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:31.068][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:31.071][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:31.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:31.075][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:31.078][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:31.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:31.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:31.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:31.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:31.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:31.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:31.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:31.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:31.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:31.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:31.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:31.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:31.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:31.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:31.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:31.112][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:31.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:31.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:31.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:31.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:31.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:31.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:31.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:31.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:31.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:31.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:31.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:31.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:31.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:31.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:31.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:31.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:31.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:31.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:31.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:31.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:31.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:31.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:31.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:31.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:31.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:31.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:31.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:31.300][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-01-31 00:49:31.303][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:31.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:31.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:31.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:31.313][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:31.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:31.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:31.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:31.322][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:31.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:31.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:31.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:31.332][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:31.355][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:31.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:31.371][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:31.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:31.376][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:31.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:31.382][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-01-31 00:49:31.384][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:31.389][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-01-31 00:49:31.392][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:31.395][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:31.397][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:31.400][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:31.403][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:31.405][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:31.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:31.415][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:31.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:31.430][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:31.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:31.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:31.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:31.440][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-01-31 00:49:31.448][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:31.451][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:31.454][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-01-31 00:49:31.875][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-01-31 00:49:32.270][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:32.275][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-01-31 00:49:32.285][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-01-31 00:49:32.313][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-01-31 00:49:32.361][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:32.365][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:32.368][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:32.373][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:32.375][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:32.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:32.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:32.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:32.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:32.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:32.401][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:32.404][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:32.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.410][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:32.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:32.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.424][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:32.427][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:32.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.433][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.521][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:32.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:32.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.533][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:32.536][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:32.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.541][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.545][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:32.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:32.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.556][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:32.560][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:32.562][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.565][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:32.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:32.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.580][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:32.584][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:32.586][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.589][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:32.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:32.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.605][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:32.609][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:32.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.614][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.617][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:32.620][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:32.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.626][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.630][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:32.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:32.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.642][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:32.646][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:32.649][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.652][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:32.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:32.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.668][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:32.671][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:32.674][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.677][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.680][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:32.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:32.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.692][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:32.695][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:32.698][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.701][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.704][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:32.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:32.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.717][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:32.733][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:32.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.739][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.743][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:32.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:32.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.754][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:32.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:32.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.763][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:32.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:32.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:32.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:32.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.785][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:32.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:32.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:32.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:32.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:32.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:32.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:32.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:32.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:32.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:32.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:32.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:32.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:32.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:32.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:32.947][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-01-31 00:49:32.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:32.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:32.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:32.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:32.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:32.970][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:32.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:32.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:32.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:32.979][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:32.981][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:32.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:32.994][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:32.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:32.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:33.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:33.004][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-01-31 00:49:33.007][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:33.011][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-01-31 00:49:33.014][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:33.017][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:33.019][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:33.022][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:33.024][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:33.026][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:33.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:33.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:33.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:33.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:33.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:33.053][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:33.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:33.057][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-01-31 00:49:33.063][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:33.065][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:33.069][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-01-31 00:49:33.482][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-01-31 00:49:33.881][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:33.885][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-01-31 00:49:33.894][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-01-31 00:49:33.900][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-01-31 00:49:33.905][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:33.908][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:33.911][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:33.915][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:33.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:33.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:33.932][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:33.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:33.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:33.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:33.946][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:33.948][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:33.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:33.953][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:33.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:33.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:33.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:33.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:33.966][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:33.968][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:33.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:33.973][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.042][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:34.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:34.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.053][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:34.056][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:34.058][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.061][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.064][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:34.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:34.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.074][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:34.077][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:34.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.081][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.084][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:34.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:34.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.095][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:34.098][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:34.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.102][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.105][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:34.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:34.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.114][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:34.116][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:34.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.120][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.123][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:34.124][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:34.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.127][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.130][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:34.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:34.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.140][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:34.142][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:34.144][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.145][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.147][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:34.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:34.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.155][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:34.158][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:34.159][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.161][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.163][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:34.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:34.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.172][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:34.175][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:34.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.180][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.183][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:34.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:34.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.193][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:34.195][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:34.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.200][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.201][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:34.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:34.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.210][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:34.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:34.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:34.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:34.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:34.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:34.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:34.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:34.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:34.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:34.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:34.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:34.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:34.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:34.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:34.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:34.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:34.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:34.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:34.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:34.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:34.396][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-01-31 00:49:34.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:34.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:34.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.408][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:34.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:34.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:34.417][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:34.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:34.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:34.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:34.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:34.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:34.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:34.439][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:34.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:34.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:34.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:34.448][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-01-31 00:49:34.450][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:34.454][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-01-31 00:49:34.457][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:34.459][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:34.462][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:34.464][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:34.466][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:34.468][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:34.474][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:34.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:34.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:34.488][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:34.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:34.492][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:34.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:34.496][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-01-31 00:49:34.501][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:34.521][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:34.524][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-01-31 00:49:34.947][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-01-31 00:49:35.353][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:35.357][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-01-31 00:49:35.365][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-01-31 00:49:35.371][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-01-31 00:49:35.375][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:35.378][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:35.381][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:35.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:35.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:35.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:35.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:35.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:35.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:35.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:35.412][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:35.415][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:35.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.419][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:35.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:35.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.433][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:35.435][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:35.437][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.440][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.506][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:35.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:35.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.516][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:35.518][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:35.520][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.522][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.525][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:35.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:35.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.535][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:35.537][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:35.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.542][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:35.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:35.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.555][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:35.557][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:35.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.562][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.565][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:35.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:35.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.574][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:35.576][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:35.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.581][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.584][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:35.586][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:35.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.590][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.593][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:35.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:35.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.602][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:35.604][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:35.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.609][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:35.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:35.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.622][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:35.625][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:35.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.630][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.633][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:35.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:35.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.641][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:35.644][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:35.646][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.649][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.652][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:35.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:35.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.661][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:35.664][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:35.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.669][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.672][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:35.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:35.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:35.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:35.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.691][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:35.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:35.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:35.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:35.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.710][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:35.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:35.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:35.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:35.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:35.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:35.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:35.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:35.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:35.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:35.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:35.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:35.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:35.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:35.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:35.860][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-01-31 00:49:35.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:35.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:35.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.873][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:35.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:35.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:35.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:35.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:35.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:35.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:35.889][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:35.891][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:35.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:35.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:35.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:35.908][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:35.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:35.913][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-01-31 00:49:35.915][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:35.919][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-01-31 00:49:35.922][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:35.925][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:35.927][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:35.930][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:35.932][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:35.934][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:35.942][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:35.944][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:35.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:35.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:35.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:35.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:35.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:35.968][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-01-31 00:49:35.974][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:35.977][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:35.980][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-01-31 00:49:36.398][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-01-31 00:49:36.796][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:36.801][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-01-31 00:49:36.809][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-01-31 00:49:36.816][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-01-31 00:49:36.820][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:36.823][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:36.825][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:36.829][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:36.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:36.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:36.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:36.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:36.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:36.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:36.854][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:36.857][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:36.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:36.861][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:36.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:36.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:36.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:36.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:36.872][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:36.875][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:36.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:36.879][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:36.946][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:36.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:36.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:36.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:36.954][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:36.957][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:36.959][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:36.961][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:36.964][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:36.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:36.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:36.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:36.973][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:36.975][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:36.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:36.979][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:36.981][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:36.983][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:36.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:36.988][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:36.990][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:36.993][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:36.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:36.997][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:37.000][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:37.003][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:37.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:37.007][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:37.010][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:37.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:37.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:37.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:37.018][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:37.020][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:37.022][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:37.024][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:37.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:37.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:37.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:37.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:37.035][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:37.038][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:37.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:37.042][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:37.044][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:37.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:37.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:37.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:37.054][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:37.056][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:37.058][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:37.061][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:37.064][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:37.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:37.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:37.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:37.073][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:37.075][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:37.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:37.080][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:37.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:37.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:37.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:37.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:37.092][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:37.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:37.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:37.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:37.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:37.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:37.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:37.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:37.110][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:37.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:37.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:37.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:37.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:37.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:37.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:37.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:37.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:37.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:37.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:37.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:37.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:37.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:37.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:37.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:37.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:37.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:37.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:37.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:37.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:37.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:37.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:37.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:37.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:37.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:37.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:37.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:37.261][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-01-31 00:49:37.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:37.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:37.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:37.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:37.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:37.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:37.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:37.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:37.281][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:37.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:37.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:37.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:37.291][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:37.292][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:37.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:37.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:37.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:37.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:37.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:37.312][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-01-31 00:49:37.314][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:37.318][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-01-31 00:49:37.321][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:37.324][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:37.326][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:37.328][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:37.330][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:37.333][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:37.339][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:37.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:37.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:37.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:37.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:37.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:37.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:37.360][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-01-31 00:49:37.367][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:37.369][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:37.372][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-01-31 00:49:37.780][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-01-31 00:49:38.172][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:38.177][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-01-31 00:49:38.185][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-01-31 00:49:38.191][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-01-31 00:49:38.195][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:38.198][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:38.201][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:38.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:38.207][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:38.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:38.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:38.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:38.223][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:38.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:38.230][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:38.232][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:38.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.236][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:38.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:38.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.248][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:38.250][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:38.253][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.255][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.326][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:38.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:38.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.335][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:38.338][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:38.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.341][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.344][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:38.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:38.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.371][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:38.374][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:38.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.378][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.380][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:38.382][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:38.385][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.387][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.389][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:38.392][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:38.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.396][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.399][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:38.401][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:38.403][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.404][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.407][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:38.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:38.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.415][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:38.417][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:38.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.422][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:38.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:38.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.433][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:38.435][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:38.437][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.439][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.442][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:38.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:38.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.451][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:38.454][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:38.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.458][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.460][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:38.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:38.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.469][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:38.471][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:38.473][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.475][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:38.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:38.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:38.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:38.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:38.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:38.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:38.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:38.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:38.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:38.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:38.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:38.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:38.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:38.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:38.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:38.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:38.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:38.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:38.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:38.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:38.658][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-01-31 00:49:38.660][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:38.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:38.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:38.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:38.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:38.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:38.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:38.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:38.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:38.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:38.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:38.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:38.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:38.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:38.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:38.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:38.713][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-01-31 00:49:38.716][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:38.719][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-01-31 00:49:38.722][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:38.725][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:38.728][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:38.730][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:38.733][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:38.735][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:38.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:38.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:38.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:38.756][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:38.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:38.761][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:38.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:38.766][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-01-31 00:49:38.773][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:38.775][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:38.779][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-01-31 00:49:39.204][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-01-31 00:49:39.606][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:39.611][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-01-31 00:49:39.619][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-01-31 00:49:39.624][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-01-31 00:49:39.628][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:39.631][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:39.634][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:39.638][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:39.640][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:39.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:39.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:39.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:39.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:39.660][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[2025-01-31 00:49:39.664][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:39.667][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:39.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.671][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:39.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:39.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.684][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:39.687][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:39.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.691][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.766][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:39.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:39.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.777][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:39.781][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:39.784][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.787][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.790][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:39.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:39.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.800][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:39.803][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:39.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.807][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.810][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:39.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:39.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.820][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:39.822][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:39.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.827][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.830][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:39.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:39.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.840][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:39.843][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:39.846][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.848][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.851][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:39.854][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:39.856][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.859][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.862][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:39.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:39.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.871][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:39.873][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:39.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.878][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:39.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:39.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.891][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:39.894][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:39.896][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.898][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.902][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:39.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:39.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.912][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:39.915][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:39.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.919][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.922][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:39.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:39.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.932][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:39.935][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:39.938][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.940][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.944][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:39.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:39.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:39.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:39.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.964][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:39.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:39.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:39.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:39.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:39.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:39.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:39.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:39.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:39.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:39.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:40.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:40.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:40.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:40.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:40.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:40.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:40.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:40.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:40.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:40.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:40.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:40.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:40.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:40.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:40.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:40.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:40.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:40.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:40.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:40.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:40.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:40.151][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-01-31 00:49:40.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:40.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:40.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:40.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:40.162][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:40.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:40.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:40.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:40.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:40.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:40.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:40.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:40.178][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:40.180][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:40.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:40.192][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:40.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:40.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:40.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:40.200][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-01-31 00:49:40.202][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:40.206][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-01-31 00:49:40.209][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:40.211][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:40.214][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:40.216][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:40.219][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:40.221][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:40.227][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:40.229][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:40.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:40.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:40.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:40.247][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:40.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:40.251][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-01-31 00:49:40.258][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:40.261][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:40.265][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-01-31 00:49:40.694][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-01-31 00:49:41.382][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:41.387][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-01-31 00:49:41.394][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-01-31 00:49:41.435][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-01-31 00:49:41.438][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:41.441][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:41.444][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:41.448][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:41.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:41.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:41.462][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:41.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:41.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:41.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:41.472][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:41.474][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:41.476][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.478][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:41.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:41.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.490][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:41.493][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:41.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.497][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.571][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:41.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:41.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.581][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:41.583][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:41.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.587][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.590][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:41.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:41.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.599][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:41.602][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:41.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.606][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.608][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:41.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:41.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.617][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:41.620][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:41.622][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.625][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.627][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:41.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:41.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.636][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:41.639][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:41.641][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.643][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.646][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:41.648][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:41.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.652][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.655][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:41.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:41.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.664][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:41.666][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:41.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.671][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:41.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:41.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.683][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:41.685][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:41.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.690][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.694][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:41.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:41.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.704][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:41.707][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:41.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.712][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.715][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:41.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:41.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.725][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:41.727][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:41.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.732][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.735][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:41.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:41.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.745][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:41.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:41.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:41.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:41.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:41.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:41.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.775][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:41.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:41.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:41.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:41.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:41.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:41.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:41.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:41.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:41.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:41.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:41.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:41.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:41.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:41.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:41.926][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-01-31 00:49:41.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:41.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:41.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.951][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:41.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:41.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:41.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:41.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:41.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:41.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:41.971][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:41.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:41.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:41.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:41.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:41.991][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:41.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:41.996][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-01-31 00:49:41.998][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:42.002][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-01-31 00:49:42.005][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:42.007][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:42.010][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:42.013][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:42.016][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:42.018][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:42.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:42.025][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:42.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:42.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:42.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:42.044][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:42.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:42.049][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-01-31 00:49:42.054][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:42.057][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:42.060][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-01-31 00:49:42.600][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-01-31 00:49:42.999][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:43.003][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-01-31 00:49:43.011][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-01-31 00:49:43.017][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-01-31 00:49:43.021][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:43.024][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:43.027][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:43.031][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:43.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:43.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:43.047][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:43.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:43.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:43.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:43.059][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:43.062][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:43.065][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.067][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:43.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:43.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.079][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:43.081][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:43.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.085][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.159][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:43.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:43.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.170][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:43.173][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:43.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.178][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.180][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:43.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:43.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.190][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:43.193][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:43.195][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.197][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.200][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:43.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:43.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.210][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:43.212][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:43.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.217][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.219][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:43.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:43.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.229][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:43.231][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:43.233][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.236][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.238][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:43.241][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:43.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.246][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.249][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:43.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:43.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.259][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:43.262][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:43.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.267][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.270][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:43.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:43.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.280][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:43.283][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:43.286][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.288][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.292][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:43.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:43.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.302][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:43.305][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:43.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.311][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.314][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:43.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:43.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.325][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:43.328][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:43.330][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.333][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.336][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:43.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:43.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.347][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:43.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:43.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.359][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:43.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:43.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:43.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:43.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:43.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:43.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:43.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:43.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:43.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:43.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:43.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:43.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:43.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:43.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:43.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:43.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:43.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:43.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:43.539][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-01-31 00:49:43.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:43.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:43.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:43.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:43.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:43.560][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:43.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:43.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:43.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:43.567][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:43.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:43.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:43.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:43.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:43.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:43.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:43.591][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-01-31 00:49:43.594][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:43.597][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-01-31 00:49:43.601][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:43.604][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:43.607][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:43.609][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:43.612][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:43.615][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:43.622][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:43.624][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:43.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:43.639][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:43.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:43.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:43.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:43.649][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-01-31 00:49:43.656][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:43.659][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:43.662][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-01-31 00:49:44.084][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-01-31 00:49:44.489][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:44.494][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-01-31 00:49:44.502][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-01-31 00:49:44.509][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-01-31 00:49:44.513][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:44.516][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:44.519][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:44.523][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:44.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:44.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:44.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:44.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:44.542][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:44.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:44.567][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:44.569][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:44.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.573][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:44.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:44.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.586][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:44.588][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:44.590][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.592][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.656][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:44.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:44.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.664][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:44.667][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:44.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.671][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.674][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:44.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:44.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.684][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:44.687][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:44.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.691][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.694][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:44.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:44.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.704][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:44.706][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:44.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.711][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.713][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:44.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:44.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.723][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:44.726][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:44.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.730][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.733][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:44.736][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:44.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.740][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.743][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:44.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:44.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.753][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:44.755][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:44.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.760][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:44.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:44.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.772][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:44.775][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:44.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.779][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:44.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:44.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.792][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:44.794][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:44.797][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.799][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.802][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:44.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:44.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.812][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:44.814][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:44.817][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.819][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.822][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:44.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:44.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:44.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:44.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:44.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:44.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:44.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:44.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.861][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:44.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:44.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:44.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:44.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:44.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:44.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:44.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:44.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:44.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:44.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:45.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:45.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:45.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:45.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:45.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:45.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:45.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:45.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:45.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:45.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:45.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:45.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:45.038][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-01-31 00:49:45.041][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:45.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:45.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:45.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:45.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:45.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:45.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:45.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:45.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:45.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:45.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:45.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:45.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:45.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:45.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:45.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:45.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:45.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:45.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:45.094][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-01-31 00:49:45.096][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:45.100][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-01-31 00:49:45.103][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:45.105][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:45.107][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:45.109][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:45.111][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:45.113][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:45.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:45.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:45.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:45.134][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:45.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:45.138][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:45.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:45.143][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-01-31 00:49:45.150][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:45.152][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:45.155][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-01-31 00:49:46.803][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-01-31 00:49:47.206][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:47.211][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-01-31 00:49:47.219][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-01-31 00:49:47.224][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-01-31 00:49:47.230][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:47.233][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:47.235][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:47.239][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:47.241][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:47.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:47.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:47.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:47.259][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:47.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:47.267][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:47.269][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:47.272][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.274][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:47.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:47.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.286][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:47.289][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:47.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.293][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.363][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:47.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:47.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.372][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:47.375][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:47.377][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.379][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.382][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:47.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:47.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.391][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:47.394][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:47.396][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.398][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.401][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:47.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:47.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.409][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:47.420][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:47.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.430][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.433][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:47.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:47.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.442][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:47.444][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:47.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.449][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.452][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:47.454][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:47.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.459][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.463][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:47.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:47.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.473][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:47.476][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:47.479][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.482][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:47.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:47.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.496][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:47.498][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:47.501][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.503][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.506][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:47.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:47.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.516][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:47.518][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:47.520][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.523][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.525][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:47.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:47.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.534][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:47.537][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:47.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.541][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.544][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:47.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:47.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:47.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:47.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:47.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:47.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:47.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:47.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:47.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:47.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:47.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:47.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:47.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:47.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:47.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:47.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:47.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:47.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:47.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:47.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:47.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:47.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:47.733][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-01-31 00:49:47.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:47.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:47.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.743][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:47.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:47.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:47.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:47.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:47.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:47.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:47.762][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:47.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:47.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:47.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:47.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:47.783][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:47.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:47.788][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-01-31 00:49:47.790][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:47.794][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-01-31 00:49:47.798][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:47.801][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:47.803][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:47.806][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:47.808][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:47.811][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:47.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:47.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:47.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:47.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:47.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:47.839][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:47.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:47.844][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-01-31 00:49:47.850][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:47.853][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:47.856][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-01-31 00:49:48.612][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-01-31 00:49:49.013][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:49.018][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-01-31 00:49:49.027][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-01-31 00:49:49.033][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-01-31 00:49:49.041][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:49.044][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:49.047][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:49.051][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:49.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:49.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:49.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:49.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:49.072][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:49.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:49.079][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:49.082][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:49.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.086][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:49.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:49.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.100][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:49.103][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:49.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.107][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.180][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:49.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:49.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.191][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:49.193][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:49.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.198][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.202][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:49.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:49.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.213][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:49.216][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:49.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.220][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.223][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:49.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:49.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.234][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:49.238][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:49.241][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.243][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.247][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:49.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:49.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.257][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:49.259][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:49.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.263][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.266][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:49.269][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:49.271][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.273][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.276][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:49.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:49.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.287][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:49.290][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:49.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.295][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:49.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:49.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.308][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:49.312][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:49.316][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.318][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.322][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:49.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:49.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.333][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:49.337][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:49.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.342][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.345][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:49.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:49.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.357][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:49.361][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:49.363][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.365][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.368][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:49.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:49.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:49.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:49.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:49.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:49.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:49.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:49.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:49.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:49.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:49.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:49.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:49.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:49.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:49.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:49.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:49.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:49.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:49.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:49.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:49.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:49.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:49.601][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-01-31 00:49:49.604][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:49.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:49.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:49.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:49.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:49.624][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:49.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:49.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:49.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:49.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:49.640][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:49.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:49.658][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:49.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:49.663][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:49.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:49.668][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-01-31 00:49:49.670][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:49.675][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-01-31 00:49:49.678][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:49.681][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:49.684][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:49.687][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:49.689][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:49.692][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:49.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:49.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:49.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:49.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:49.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:49.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:49.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:49.730][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-01-31 00:49:49.736][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:49.738][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:49.741][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-01-31 00:49:50.156][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-01-31 00:49:50.558][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:50.562][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-01-31 00:49:50.571][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-01-31 00:49:50.577][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-01-31 00:49:50.582][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:50.585][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:50.588][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:50.592][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:50.594][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:50.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:50.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:50.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:50.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:50.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:50.620][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:50.622][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:50.625][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.627][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:50.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:50.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.641][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:50.643][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:50.646][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.648][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.719][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:50.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:50.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.730][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:50.733][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:50.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.735][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.738][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:50.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:50.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.746][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:50.749][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:50.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.753][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.756][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:50.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:50.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.766][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:50.768][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:50.770][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.772][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:50.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:50.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.783][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:50.785][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:50.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.787][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.790][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:50.792][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:50.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.797][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.800][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:50.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:50.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.811][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:50.813][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:50.816][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.818][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:50.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:50.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.830][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:50.833][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:50.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.848][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.851][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:50.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:50.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.861][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:50.864][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:50.866][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.869][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.872][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:50.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:50.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.882][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:50.885][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:50.887][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.890][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.893][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:50.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:50.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:50.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:50.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:50.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:50.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:50.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:50.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:50.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:50.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:50.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:50.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:50.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:50.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:50.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:50.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:50.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:50.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:51.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:51.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:51.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:51.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:51.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:51.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:51.101][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-01-31 00:49:51.109][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:51.182][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:49:51.190][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-31 00:49:51.193][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-31 00:49:51.197][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-31 00:49:51.200][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-01-31 00:49:51.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:51.209][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:51.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:51.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:51.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:51.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:51.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:51.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.250][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:51.261][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:51.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:51.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:51.277][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:51.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:51.282][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:51.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:51.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.313][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.333][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:51.344][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:51.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:51.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:51.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:51.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:51.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:51.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:51.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:51.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:51.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:51.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:51.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:51.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:51.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:51.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:51.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.478][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.503][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:51.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:51.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:51.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:51.537][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:51.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:51.543][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:51.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:51.548][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.585][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:51.601][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:51.603][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:51.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:51.618][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:51.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:51.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:51.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:51.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.651][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:51.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:51.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:51.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:51.727][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:51.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:51.733][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:51.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:51.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.756][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:51.813][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:51.815][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:51.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:51.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:51.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:51.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:51.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:51.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.861][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.873][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:51.886][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:51.888][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:51.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:51.901][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:51.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:51.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:51.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:51.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.940][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:51.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:51.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:51.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:51.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:51.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:51.975][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:51.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:51.982][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:51.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:51.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:51.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:52.014][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:52.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:52.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:52.034][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:52.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:52.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:52.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:52.046][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.102][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:52.116][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:52.118][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:52.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:52.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:52.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:52.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:52.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:52.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.159][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:52.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:52.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:52.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:52.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:52.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:52.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:52.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:52.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.230][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:52.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:52.264][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:52.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:52.278][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:52.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:52.283][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:52.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:52.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.298][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.308][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:52.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:52.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:52.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:52.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:52.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:52.339][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:52.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:52.344][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.355][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.365][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:52.376][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:52.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:52.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:52.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:52.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:52.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:52.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:52.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.410][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.419][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:52.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:52.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:52.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:52.444][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:52.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:52.449][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:52.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:52.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:52.488][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:52.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:52.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:52.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:52.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:52.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:52.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:52.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.525][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:52.546][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:52.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:52.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:52.562][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:52.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:52.566][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:52.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:52.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.581][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.590][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:52.601][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:52.603][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:52.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:52.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:52.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:52.622][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:52.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:52.627][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.647][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:52.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:52.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:52.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:52.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:52.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:52.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:52.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:52.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:52.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:52.733][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:52.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:52.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:52.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:52.812][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:49:52.821][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:52.823][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:52.827][private$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[2025-01-31 00:49:53.225][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[2025-01-31 00:49:53.620][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:53.624][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-01-31 00:49:53.633][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-01-31 00:49:53.641][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[2025-01-31 00:49:53.649][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:53.651][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:53.656][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-01-31 00:49:54.054][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-01-31 00:49:54.454][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:54.459][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-01-31 00:49:54.468][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-01-31 00:49:54.474][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:54.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:54.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:54.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:54.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:54.495][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:54.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:54.500][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-01-31 00:49:54.503][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:54.507][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-01-31 00:49:54.510][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:54.513][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:54.516][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:54.518][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:54.521][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:54.523][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:54.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:54.533][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:54.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:54.546][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:54.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:54.550][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:54.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:54.555][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-01-31 00:49:54.562][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:54.564][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:54.568][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-01-31 00:49:54.990][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-01-31 00:49:55.403][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:55.408][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-01-31 00:49:55.416][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-01-31 00:49:55.422][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-01-31 00:49:55.426][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:55.429][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:55.432][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:55.435][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:55.437][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:55.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:55.450][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:55.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:55.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:55.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:55.460][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:55.462][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:55.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.464][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:55.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:55.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.476][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:55.478][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:55.480][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.483][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.575][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:55.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:55.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.585][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:55.587][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:55.590][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.592][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.595][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:55.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:55.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.605][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:55.607][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:55.609][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.611][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.614][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:55.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:55.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.623][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:55.626][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:55.628][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.631][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.634][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:55.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:55.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.643][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:55.646][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:55.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.650][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.653][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:55.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:55.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.662][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:55.664][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:55.667][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.669][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.671][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:55.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:55.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.681][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:55.684][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:55.686][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.688][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.691][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:55.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:55.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.701][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:55.703][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:55.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.709][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.712][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:55.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:55.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.721][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:55.723][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:55.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.727][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.730][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:55.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:55.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.739][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:55.742][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:55.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.746][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.749][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:55.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:55.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.758][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:55.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:55.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:55.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:55.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:55.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:55.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:55.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:55.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:55.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:55.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:55.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:55.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:55.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:55.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:55.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:55.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:55.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:55.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:55.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:55.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:55.944][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-01-31 00:49:55.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:55.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:55.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:55.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:55.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:55.965][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:55.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:55.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:55.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:55.974][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:55.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:55.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:55.988][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:55.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:55.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:55.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:55.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:56.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:56.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:56.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:56.007][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:56.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:56.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:56.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:56.017][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:56.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:56.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:56.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:56.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:56.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:56.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:56.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:56.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:56.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:56.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:56.052][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-01-31 00:49:56.054][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:49:56.058][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-01-31 00:49:56.061][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:49:56.063][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:49:56.066][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:49:56.068][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:49:56.071][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:49:56.073][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:49:56.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:56.081][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:56.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:56.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:56.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:56.099][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:56.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:49:56.103][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-01-31 00:49:56.110][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:49:56.113][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:49:56.116][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-01-31 00:49:56.537][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-01-31 00:49:56.950][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:49:56.954][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-01-31 00:49:56.963][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-01-31 00:49:56.969][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-01-31 00:49:56.973][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:49:56.976][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:49:56.979][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:49:56.983][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:56.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:56.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:57.000][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:57.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:57.005][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:57.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:57.013][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:57.016][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:57.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.021][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:57.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:57.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.035][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:57.037][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:57.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.042][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.114][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:49:57.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:49:57.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.124][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:57.126][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:57.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.131][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.134][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:49:57.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:49:57.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.144][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:57.147][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:57.149][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.151][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.154][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:49:57.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:49:57.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.164][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:57.167][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:57.169][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.171][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.188][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:49:57.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:49:57.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.197][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:57.200][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:49:57.202][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.204][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.207][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:57.210][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:57.212][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.214][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.217][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:49:57.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:49:57.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.226][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.229][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.233][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.245][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:57.247][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:57.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.251][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.255][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:49:57.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:49:57.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.264][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:57.267][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:57.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.272][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.275][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:49:57.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:49:57.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.284][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:57.287][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:57.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.291][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.294][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:49:57.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:49:57.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:57.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:57.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:57.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:57.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:57.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:57.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:49:57.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:49:57.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:57.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:57.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:57.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:57.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:57.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:57.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:57.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:57.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:57.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:57.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:49:57.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:49:57.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:57.513][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-01-31 00:49:57.515][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.536][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:57.594][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:49:57.602][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-31 00:49:57.605][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-31 00:49:57.608][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-31 00:49:57.611][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-01-31 00:49:57.618][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:57.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:57.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:57.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:57.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:57.637][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:57.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:57.642][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.652][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:57.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:57.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:57.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:57.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:57.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:57.689][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:57.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:57.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:57.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:57.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:57.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:57.756][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:57.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:57.760][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:57.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:57.765][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:57.820][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:57.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:57.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:57.835][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:57.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:57.840][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:57.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:57.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:57.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:57.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:57.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:57.905][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:57.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:57.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:57.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:57.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:57.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:57.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:57.957][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:57.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:57.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:57.985][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:57.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:57.990][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:57.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:57.995][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:57.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.016][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:58.027][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:58.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:58.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:58.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:58.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:58.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:58.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:58.055][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:58.099][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:58.101][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:58.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:58.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:58.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:58.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:58.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:58.127][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.140][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:58.165][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:58.169][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:58.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:58.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:58.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:58.190][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:58.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:58.196][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:58.235][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:58.240][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:58.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:58.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:58.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:58.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:58.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:58.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:58.304][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:58.306][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:58.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:58.358][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:58.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:58.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:58.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:58.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.432][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:58.489][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:58.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:58.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:58.511][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:58.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:58.516][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:58.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:58.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:58.611][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:58.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:58.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:58.626][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:58.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:58.630][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:58.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:58.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:58.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:58.682][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:58.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:58.702][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:58.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:58.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:58.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:58.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:58.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:58.748][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:58.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:58.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:58.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:58.783][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:58.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:58.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:58.822][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:58.856][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:58.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:58.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:58.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:58.879][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:58.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:58.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.897][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:58.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:58.959][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:58.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:58.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:58.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:58.984][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:58.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:58.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:58.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:58.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:58.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:59.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:59.020][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:59.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:59.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:59.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:59.043][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:59.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:59.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:59.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:59.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:59.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:59.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:59.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:59.115][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:59.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:59.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:59.168][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:59.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:59.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:59.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:59.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:59.193][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:59.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:59.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.211][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.221][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:59.287][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:49:59.296][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-31 00:49:59.299][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-31 00:49:59.303][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-31 00:49:59.306][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-01-31 00:49:59.314][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:59.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:59.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:59.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:59.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:59.337][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:59.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:59.342][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:59.393][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:59.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:59.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:59.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:59.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:59.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:59.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:59.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:59.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:59.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:59.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:59.509][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:59.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:59.513][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:59.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:59.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.550][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:59.572][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:59.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:59.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:59.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:59.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:59.591][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:59.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:59.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.632][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:59.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:59.644][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:59.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:59.657][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:59.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:59.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:59.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:59.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:59.695][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:59.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:59.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:59.709][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:59.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:59.714][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:59.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:59.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:59.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:59.748][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:59.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:59.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:59.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:59.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:59.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:59.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:59.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:59.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:59.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:59.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:59.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:59.834][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:59.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:59.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:59.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:59.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:59.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:59.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:59.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:59.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:59.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:59.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:59.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:59.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:59.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:59.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:59.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:59.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:59.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:59.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.955][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:49:59.965][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:49:59.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:49:59.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:49:59.974][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:49:59.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:49:59.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:49:59.989][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:49:59.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:49:59.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:49:59.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:49:59.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:00.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:00.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:00.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:00.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:00.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:00.048][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:00.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:00.054][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:00.088][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:00.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:00.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:00.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:00.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:00.107][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:00.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:00.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:00.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:00.141][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:00.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:00.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:00.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:00.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:00.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:00.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.173][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.182][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:00.191][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:00.193][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:00.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:00.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:00.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:00.210][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:00.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:00.215][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:00.245][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:00.247][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:00.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:00.260][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:00.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:00.265][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:00.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:00.270][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:00.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:00.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:00.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:00.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:00.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:00.328][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:00.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:00.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.342][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.352][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:00.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:00.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:00.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:00.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:00.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:00.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:00.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:00.384][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.403][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:00.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:00.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:00.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:00.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:00.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:00.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:00.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:00.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:00.465][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:00.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:00.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:00.480][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:00.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:00.484][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:00.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:00.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.498][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:00.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.554][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-01-31 00:50:00.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-01-31 00:50:00.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-31 00:50:00.582][biodb::testThat]
biodb.INFO [2025-01-31 00:50:00.584][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-01-31 00:50:00.586][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:50:00.588][biodb::testThat]
biodb.TRACE[2025-01-31 00:50:00.595][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-31 00:50:00.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-31 00:50:00.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.604][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.623][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:00.648][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:00.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:00.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:00.664][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:00.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:00.669][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:00.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:00.678][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:50:00.685][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-31 00:50:00.688][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-01-31 00:50:00.691][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-31 00:50:00.694][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-01-31 00:50:00.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:00.701][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:00.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:00.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:00.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:00.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:00.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:00.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.741][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:00.752][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:50:00.760][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-31 00:50:00.763][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-01-31 00:50:00.765][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-31 00:50:00.769][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-01-31 00:50:00.773][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:00.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:00.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:00.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:00.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:00.793][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:00.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:00.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.817][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:00.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:00.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:00.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:00.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:00.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:00.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:00.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:00.857][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.867][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:00.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:00.887][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-31 00:50:00.891][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:00.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:00.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:00.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:00.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:00.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:00.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:00.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:00.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:00.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:00.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:00.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.934][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:00.936][private$selectFields]
biodb.TRACE[2025-01-31 00:50:00.938][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-31 00:50:00.941][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-31 00:50:00.943][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:00.946][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:00.949][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:00.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.954][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.956][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:00.959][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:00.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.963][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.966][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:00.968][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:00.970][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:00.973][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:00.975][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.978][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.980][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-31 00:50:00.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:00.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:00.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:00.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:00.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:00.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:00.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:01.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:01.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:01.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:01.038][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-01-31 00:50:01.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:01.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:01.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:01.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:01.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:01.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:01.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:01.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:01.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:01.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:01.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:01.082][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:01.084][private$selectFields]
biodb.TRACE[2025-01-31 00:50:01.086][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-31 00:50:01.088][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-31 00:50:01.090][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:01.093][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.095][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.097][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:01.099][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:01.101][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.103][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:01.107][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:01.110][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:01.113][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:01.115][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.117][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:01.122][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:01.124][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-31 00:50:01.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:01.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:01.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:01.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:01.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:01.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:01.162][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-31 00:50:01.165][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:01.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:01.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:01.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:01.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:01.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:01.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:01.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:01.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:01.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:01.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:01.205][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:01.207][private$selectFields]
biodb.TRACE[2025-01-31 00:50:01.209][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-31 00:50:01.212][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-31 00:50:01.214][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:01.216][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.218][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:01.222][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:01.224][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.227][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.229][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:01.231][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:01.233][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:01.235][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:01.237][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.240][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:01.244][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:01.246][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-31 00:50:01.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:01.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:01.257][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:01.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:01.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:01.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:01.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:01.276][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-01-31 00:50:01.278][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-31 00:50:01.280][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-31 00:50:01.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:01.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:01.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:01.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:01.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:01.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:01.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:01.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:01.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:01.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:01.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:01.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:01.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:01.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:01.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:01.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:01.483][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:01.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:01.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:01.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:01.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:01.501][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:01.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:01.510][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:50:01.517][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:50:01.520][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:50:01.524][private$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[2025-01-31 00:50:01.926][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[2025-01-31 00:50:02.320][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:50:02.324][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-01-31 00:50:02.334][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-01-31 00:50:02.341][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[2025-01-31 00:50:02.349][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:50:02.351][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:50:02.356][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-01-31 00:50:02.764][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-01-31 00:50:03.763][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:50:03.767][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-01-31 00:50:03.777][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-01-31 00:50:03.784][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:03.786][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:03.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:03.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:03.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:03.806][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:03.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:03.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:03.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:03.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:03.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:03.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:03.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:03.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:03.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:03.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:03.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:03.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:03.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:03.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:03.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:03.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:03.855][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:03.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:03.860][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:03.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:03.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:03.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:03.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:03.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:03.874][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:03.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:03.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:03.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:03.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:03.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:03.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:03.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:03.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:03.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:03.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:03.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:03.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:03.915][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:03.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:03.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:03.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:03.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:03.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:03.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:03.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:03.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:03.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:03.939][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:03.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:03.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:03.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:04.014][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-31 00:50:04.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:04.084][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:04.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:04.099][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:04.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:04.104][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:04.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:04.110][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.120][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.130][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:04.132][private$selectFields]
biodb.TRACE[2025-01-31 00:50:04.154][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-31 00:50:04.157][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-31 00:50:04.159][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:04.161][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.164][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.169][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.171][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.173][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.178][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.180][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:04.183][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:04.185][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.188][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.191][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.193][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.195][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-31 00:50:04.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.229][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-01-31 00:50:04.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:04.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:04.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:04.247][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:04.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:04.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:04.254][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.TRACE[2025-01-31 00:50:04.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.366][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:04.368][private$selectFields]
biodb.TRACE[2025-01-31 00:50:04.371][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-31 00:50:04.373][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-31 00:50:04.376][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:04.378][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.381][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.386][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.388][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.390][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.394][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.397][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:04.424][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:04.427][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.430][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.434][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.436][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-31 00:50:04.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.469][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-31 00:50:04.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:04.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:04.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:04.487][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:04.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:04.491][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:04.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:04.496][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.514][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:04.517][private$selectFields]
biodb.TRACE[2025-01-31 00:50:04.519][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-31 00:50:04.521][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-31 00:50:04.523][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:04.525][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.528][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.530][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.532][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.534][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.538][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.542][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.544][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:04.547][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:04.549][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.551][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.554][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.556][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.558][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-31 00:50:04.561][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:04.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.590][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-01-31 00:50:04.592][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-31 00:50:04.595][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-31 00:50:04.615][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-01-31 00:50:04.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-01-31 00:50:04.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-31 00:50:04.632][biodb::testThat]
biodb.INFO [2025-01-31 00:50:04.634][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-01-31 00:50:04.637][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:50:04.639][biodb::testThat]
biodb.TRACE[2025-01-31 00:50:04.646][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-31 00:50:04.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-31 00:50:04.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.675][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:04.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:04.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:04.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:04.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:04.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:04.720][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:04.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:04.729][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:50:04.736][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-31 00:50:04.740][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-01-31 00:50:04.743][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-31 00:50:04.746][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-01-31 00:50:04.751][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:04.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:04.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:04.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:04.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:04.794][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:04.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:04.799][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.810][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:04.835][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:50:04.844][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-31 00:50:04.847][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-01-31 00:50:04.850][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-31 00:50:04.853][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-01-31 00:50:04.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:04.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:04.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:04.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:04.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:04.879][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:04.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:04.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.894][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.904][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:04.913][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:04.915][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:04.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:04.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:04.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:04.932][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:04.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:04.937][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:04.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:04.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:04.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:04.966][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-31 00:50:04.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:04.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:04.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:04.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:04.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:04.995][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:04.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:05.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.073][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:05.075][private$selectFields]
biodb.TRACE[2025-01-31 00:50:05.077][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-31 00:50:05.081][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-31 00:50:05.083][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:05.086][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.088][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.093][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.095][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.098][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.103][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.105][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:05.107][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:05.110][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.112][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.117][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.119][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-31 00:50:05.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.152][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-01-31 00:50:05.155][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:05.157][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:05.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:05.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:05.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:05.173][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:05.176][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[2025-01-31 00:50:05.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.197][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:05.199][private$selectFields]
biodb.TRACE[2025-01-31 00:50:05.201][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-31 00:50:05.203][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-31 00:50:05.205][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:05.208][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.210][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.213][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.215][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.217][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.219][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.224][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.226][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:05.229][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:05.231][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.234][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.236][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.238][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.241][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-31 00:50:05.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.253][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.262][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.272][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-31 00:50:05.275][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:05.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:05.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:05.290][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:05.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:05.294][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:05.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:05.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.318][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:05.320][private$selectFields]
biodb.TRACE[2025-01-31 00:50:05.322][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-31 00:50:05.324][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-31 00:50:05.327][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:05.329][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.332][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.336][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.338][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.341][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.343][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.345][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.348][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:05.350][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:05.352][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.355][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.359][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.362][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-31 00:50:05.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.374][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.384][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.395][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-01-31 00:50:05.398][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-31 00:50:05.400][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-31 00:50:05.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.432][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:05.466][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:05.468][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:05.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:05.481][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:05.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:05.485][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:05.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:05.494][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:50:05.502][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-31 00:50:05.505][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-01-31 00:50:05.508][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-31 00:50:05.511][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-01-31 00:50:05.518][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:50:05.526][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-31 00:50:05.530][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-01-31 00:50:05.533][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-31 00:50:05.536][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-01-31 00:50:05.541][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:05.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:05.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:05.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:05.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:05.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:05.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:05.568][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:05.598][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:05.600][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:05.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:05.614][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:05.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:05.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:05.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:05.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.632][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:05.652][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:05.654][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:05.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:05.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:05.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:05.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:05.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:05.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:05.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:05.706][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-31 00:50:05.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:05.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:05.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:05.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:05.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:05.729][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:05.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:05.734][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.745][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.760][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:05.762][private$selectFields]
biodb.TRACE[2025-01-31 00:50:05.764][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-31 00:50:05.767][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-31 00:50:05.769][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:05.772][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.774][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.779][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.781][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.784][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.788][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.790][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:05.792][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:05.795][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.797][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.801][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.803][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-31 00:50:05.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.835][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.847][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-01-31 00:50:05.851][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:05.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:05.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:05.869][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:05.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:05.873][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:05.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:05.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.887][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.895][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:05.897][private$selectFields]
biodb.TRACE[2025-01-31 00:50:05.899][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-31 00:50:05.901][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-31 00:50:05.903][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:05.906][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.910][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.915][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.918][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.920][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.923][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.925][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.928][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:05.930][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:05.933][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.935][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.938][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.940][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.943][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-31 00:50:05.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.963][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:05.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:05.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:05.974][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-31 00:50:05.977][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:05.979][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:05.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:05.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:05.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:05.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:06.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:06.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:06.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:06.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:06.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:06.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:06.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:06.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:06.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:06.022][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:06.024][private$selectFields]
biodb.TRACE[2025-01-31 00:50:06.026][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-31 00:50:06.029][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-31 00:50:06.031][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:06.033][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:06.036][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:06.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:06.041][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:06.043][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:06.046][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:06.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:06.050][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:06.053][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:06.055][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:06.057][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:06.060][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:06.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:06.065][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:06.067][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-31 00:50:06.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:06.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:06.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:06.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:06.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:06.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:06.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:06.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:06.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:06.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:06.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:06.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:06.096][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-01-31 00:50:06.098][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-31 00:50:06.100][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-31 00:50:06.121][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-01-31 00:50:06.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-01-31 00:50:06.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:06.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-31 00:50:06.138][biodb::testThat]
biodb.INFO [2025-01-31 00:50:06.140][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-01-31 00:50:06.142][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:50:06.144][biodb::testThat]
biodb.TRACE[2025-01-31 00:50:06.150][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-31 00:50:06.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-31 00:50:06.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:06.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:06.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:06.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:06.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:06.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:06.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:06.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:06.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:06.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:06.179][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:06.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:06.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:06.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:06.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:06.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:06.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:06.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:06.206][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:06.209][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:06.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:06.245][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:06.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:06.249][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:06.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:06.258][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.INFO [2025-01-31 00:50:06.266][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2025-01-31 00:50:06.269][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:50:06.271][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:50:06.275][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-01-31 00:50:06.676][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-01-31 00:50:07.072][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:50:07.076][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-01-31 00:50:07.085][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-01-31 00:50:07.091][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:07.093][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:07.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:07.106][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:07.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:07.110][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:07.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:07.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:07.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:07.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:07.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:07.124][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:07.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:07.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:07.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:07.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:07.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:07.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:07.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:07.145][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:50:07.153][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:50:07.155][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:50:07.159][private$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[2025-01-31 00:50:07.563][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[2025-01-31 00:50:07.961][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:50:07.966][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-01-31 00:50:07.975][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-01-31 00:50:07.981][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:07.983][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:07.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:07.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:07.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:07.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:08.001][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[2025-01-31 00:50:08.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:08.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:08.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.013][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:08.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:08.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:08.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:08.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:08.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:08.032][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:08.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:08.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:08.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:08.048][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:08.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:08.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:08.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:08.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:08.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:08.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.071][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:08.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:08.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:08.080][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-31 00:50:08.083][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:08.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:08.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:08.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:08.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:08.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:08.104][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.TRACE[2025-01-31 00:50:08.107][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.116][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.124][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:08.126][private$selectFields]
biodb.TRACE[2025-01-31 00:50:08.129][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-31 00:50:08.131][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-31 00:50:08.133][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:08.135][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.137][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.139][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.140][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.142][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.145][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.147][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.149][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.151][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:08.153][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:08.154][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.157][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.159][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.161][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.163][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-31 00:50:08.165][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.194][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-01-31 00:50:08.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:08.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:08.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:08.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:08.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:08.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:08.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:08.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.256][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.265][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:08.267][private$selectFields]
biodb.TRACE[2025-01-31 00:50:08.269][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-31 00:50:08.271][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-31 00:50:08.273][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:08.275][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.278][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.282][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.284][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.286][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.291][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.293][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:08.296][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:08.299][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.301][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.305][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.308][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-31 00:50:08.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.337][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-31 00:50:08.339][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:08.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:08.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:08.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:08.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:08.358][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:08.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:08.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.380][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:08.383][private$selectFields]
biodb.TRACE[2025-01-31 00:50:08.385][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-31 00:50:08.387][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-31 00:50:08.390][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:08.392][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.395][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.397][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.399][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.401][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.403][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.407][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.409][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:08.412][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:08.414][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.416][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.421][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.423][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-31 00:50:08.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.443][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:08.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.453][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-01-31 00:50:08.455][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-31 00:50:08.457][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-31 00:50:08.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:08.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:08.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.515][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:08.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:08.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:08.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:08.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:08.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:08.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:08.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:08.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:08.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:08.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:08.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:08.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:08.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:08.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:08.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:08.579][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[2025-01-31 00:50:08.587][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:50:08.590][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:50:08.595][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-01-31 00:50:08.995][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-01-31 00:50:09.400][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:50:09.404][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-01-31 00:50:09.455][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-01-31 00:50:09.500][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:50:09.509][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:50:09.513][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:50:09.518][private$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[2025-01-31 00:50:09.920][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[2025-01-31 00:50:10.316][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:50:10.320][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-01-31 00:50:10.329][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-01-31 00:50:10.336][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:10.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:10.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:10.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:10.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:10.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:10.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:10.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:10.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:10.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:10.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:10.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:10.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:10.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:10.389][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:10.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:10.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:10.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:10.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:10.409][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:10.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:10.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:10.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:10.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:10.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:10.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:10.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:10.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:10.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:10.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:10.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:10.455][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:10.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:10.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:10.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:10.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:10.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:10.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:10.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:10.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:10.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:10.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:10.490][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-31 00:50:10.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:10.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:10.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:10.508][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:10.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:10.512][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:10.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:10.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.534][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:10.536][private$selectFields]
biodb.TRACE[2025-01-31 00:50:10.538][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-31 00:50:10.540][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-31 00:50:10.542][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:10.544][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.547][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.551][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.554][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.556][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.558][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.561][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.563][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:10.565][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:10.568][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.570][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.573][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.575][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.577][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-31 00:50:10.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.610][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-01-31 00:50:10.613][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:10.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:10.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:10.629][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:10.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:10.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:10.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:10.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.657][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:10.659][private$selectFields]
biodb.TRACE[2025-01-31 00:50:10.662][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-31 00:50:10.664][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-31 00:50:10.667][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:10.670][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.673][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.678][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.680][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.683][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.685][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.687][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.690][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:10.692][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:10.695][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.697][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.702][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.704][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-31 00:50:10.706][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.715][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.753][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-31 00:50:10.756][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:10.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:10.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:10.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:10.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:10.774][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:10.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:10.778][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.796][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:10.798][private$selectFields]
biodb.TRACE[2025-01-31 00:50:10.800][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-31 00:50:10.802][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-31 00:50:10.805][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:10.808][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.810][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.815][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.817][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.820][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.824][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.826][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:10.829][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-31 00:50:10.831][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.833][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.838][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.840][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-31 00:50:10.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:10.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:10.870][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-01-31 00:50:10.872][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-31 00:50:10.874][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-31 00:50:10.920][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-01-31 00:50:10.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-01-31 00:50:10.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:10.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-31 00:50:10.937][biodb::testThat]
biodb.INFO [2025-01-31 00:50:10.939][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-01-31 00:50:10.941][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:50:10.943][biodb::testThat]
biodb.DEBUG[2025-01-31 00:50:10.947][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-01-31 00:50:10.949][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:50:10.953][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-01-31 00:50:10.956][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:50:10.958][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:50:10.961][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:50:10.963][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:50:10.965][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:50:10.975][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:50:10.982][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:10.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:11.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:11.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:11.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:11.018][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:11.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:11.027][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-01-31 00:50:11.033][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:50:11.036][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:50:11.039][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-01-31 00:50:11.437][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-01-31 00:50:11.835][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:50:11.839][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-01-31 00:50:11.852][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-01-31 00:50:11.858][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-01-31 00:50:11.861][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:50:11.866][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:50:11.869][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:50:11.872][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:11.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:11.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:11.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:11.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:11.891][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:11.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:11.898][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:11.900][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:11.902][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:11.904][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:11.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:11.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:11.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:11.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:11.917][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:50:11.919][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:50:11.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:11.923][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:11.926][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:50:11.929][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:50:11.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:11.934][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:11.937][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:50:11.940][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:50:11.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:11.944][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:11.946][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:50:11.949][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:50:11.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:11.953][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:11.956][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:50:11.959][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:50:11.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:11.963][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:11.966][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:50:11.968][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:11.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:11.972][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:11.975][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:11.977][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:11.980][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:11.982][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:11.984][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:50:11.987][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:50:11.989][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:11.991][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:11.995][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:50:11.997][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:50:11.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:12.001][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:12.004][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:50:12.006][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:50:12.008][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:12.010][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:12.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:12.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:12.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:12.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:12.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:12.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:12.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:12.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:12.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:12.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:12.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:12.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:12.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:12.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:12.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:12.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:12.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:12.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:12.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:12.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:12.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:12.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:12.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:12.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:12.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:12.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:12.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:12.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:12.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:12.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:12.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:12.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:12.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:12.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:12.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:12.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:12.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:12.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:12.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:12.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:12.262][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-01-31 00:50:12.265][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-01-31 00:50:12.283][biodb::testThat]
biodb.INFO [2025-01-31 00:50:12.286][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-01-31 00:50:12.288][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:50:12.290][biodb::testThat]
biodb.DEBUG[2025-01-31 00:50:12.313][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-01-31 00:50:12.315][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-01-31 00:50:12.318][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-01-31 00:50:12.321][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.INFO [2025-01-31 00:50:12.324][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-01-31 00:50:12.327][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-01-31 00:50:12.329][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:50:12.332][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:50:12.334][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:50:12.337][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:50:12.340][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:50:12.350][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:12.352][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:12.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:12.381][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:12.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:12.385][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:12.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:12.389][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-01-31 00:50:12.396][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:50:12.398][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:50:12.401][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-01-31 00:50:12.799][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-01-31 00:50:13.199][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:50:13.204][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-01-31 00:50:13.213][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-01-31 00:50:13.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:13.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:13.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:13.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:13.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:13.237][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:13.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:13.244][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-01-31 00:50:13.252][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:50:13.254][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:50:13.258][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-01-31 00:50:13.676][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-01-31 00:50:14.077][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:50:14.081][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-01-31 00:50:14.089][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-01-31 00:50:14.092][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:14.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:14.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:14.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:14.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:14.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:14.115][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[2025-01-31 00:50:14.118][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-01-31 00:50:14.124][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:50:14.127][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:50:14.131][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-01-31 00:50:14.549][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-01-31 00:50:14.952][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:50:14.958][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-01-31 00:50:14.972][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-01-31 00:50:14.980][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-01-31 00:50:14.985][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:50:14.993][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-01-31 00:50:14.998][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-01-31 00:50:15.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:15.009][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:15.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:15.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:15.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:15.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:15.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:15.035][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:15.038][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:15.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.042][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:15.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:15.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.055][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:50:15.057][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:50:15.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.061][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.064][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:50:15.066][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:50:15.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.071][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.074][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:50:15.077][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:50:15.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.082][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.084][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:50:15.087][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:50:15.089][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.092][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.094][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:50:15.097][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:50:15.099][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.101][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.104][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:50:15.107][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:15.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.111][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.114][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:15.117][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:15.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.121][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.124][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:50:15.126][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:50:15.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.131][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.134][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:50:15.137][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:50:15.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.142][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.145][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:50:15.147][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:50:15.149][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.152][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:15.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:15.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.165][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:15.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:15.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:15.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:15.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.252][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:15.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:15.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:15.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:15.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:15.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:15.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:15.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:15.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:15.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:15.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:15.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:15.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:15.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:15.312][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:15.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:15.319][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:15.322][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:15.325][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.327][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:15.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:15.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.340][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:50:15.343][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:50:15.346][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.348][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.351][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:50:15.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:50:15.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.361][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:50:15.364][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:50:15.366][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.369][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.372][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:50:15.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:50:15.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.382][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:50:15.385][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:50:15.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.390][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.392][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:50:15.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:50:15.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.403][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:50:15.406][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:50:15.408][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.411][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.414][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:50:15.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:50:15.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.425][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:50:15.427][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:50:15.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.432][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.435][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:50:15.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:50:15.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.445][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:50:15.448][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:15.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.452][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.455][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:50:15.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:15.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.466][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:15.468][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:15.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.473][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:15.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:15.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.486][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:50:15.489][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:50:15.491][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.496][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.500][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:50:15.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:50:15.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.512][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:50:15.515][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:50:15.517][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.520][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.523][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:50:15.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:50:15.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.533][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:50:15.535][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:50:15.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.540][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.543][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:50:15.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:50:15.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:15.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:15.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:15.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:15.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:15.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:15.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:15.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:15.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:15.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:15.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:15.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:15.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:15.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:15.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:15.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:15.627][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:15.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:15.641][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:15.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:15.646][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:15.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-31 00:50:15.654][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:15.657][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:15.659][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.662][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:15.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:15.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.702][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:50:15.704][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:50:15.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.709][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.712][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:50:15.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:50:15.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.723][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:50:15.726][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:50:15.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.731][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.734][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:50:15.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:50:15.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.743][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:50:15.746][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:50:15.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.751][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.753][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:50:15.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:50:15.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.763][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:50:15.765][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:50:15.767][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.769][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.772][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:50:15.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:50:15.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.781][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:50:15.784][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:50:15.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.788][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.791][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:50:15.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:50:15.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.800][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:50:15.802][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:15.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.807][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.809][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:50:15.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:15.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.818][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:15.821][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:15.823][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.825][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:15.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:15.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.837][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:50:15.840][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:50:15.842][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.844][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.847][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:50:15.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:50:15.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.856][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:50:15.859][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:50:15.861][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.864][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.867][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:50:15.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:50:15.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.878][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:50:15.881][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:50:15.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.887][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.889][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:50:15.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:50:15.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.899][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:15.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:15.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:15.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:15.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:15.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:15.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:15.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:15.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:15.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:15.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:15.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:15.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:15.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:15.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:15.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:15.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:16.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:16.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:16.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:16.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:16.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:16.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:16.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:16.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:16.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:16.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:16.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:16.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:16.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:16.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:16.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:16.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:16.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:16.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:16.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:16.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:16.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:16.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:16.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:16.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:16.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:16.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:16.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:16.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:16.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:16.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:16.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:16.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:16.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:16.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:16.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:16.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:16.170][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-01-31 00:50:16.172][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-01-31 00:50:16.174][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-01-31 00:50:16.207][biodb::testThat]
biodb.INFO [2025-01-31 00:50:16.210][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-01-31 00:50:16.212][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:50:16.215][biodb::testThat]
biodb.INFO [2025-01-31 00:50:16.277][biodb::testThat]
biodb.INFO [2025-01-31 00:50:16.279][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-01-31 00:50:16.281][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:50:16.283][biodb::testThat]
biodb.INFO [2025-01-31 00:50:16.303][biodb::testThat]
biodb.INFO [2025-01-31 00:50:16.306][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-01-31 00:50:16.308][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:50:16.309][biodb::testThat]
biodb.DEBUG[2025-01-31 00:50:16.315][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:50:16.322][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:50:16.325][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:50:16.329][private$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[2025-01-31 00:50:16.885][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[2025-01-31 00:50:17.409][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:50:17.413][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-01-31 00:50:17.423][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-01-31 00:50:17.450][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:50:17.453][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:50:17.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:17.457][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:17.459][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:17.461][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:17.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:17.466][ef$get] fields variable is a list.
biodb.INFO [2025-01-31 00:50:17.469][biodb::testThat]
biodb.INFO [2025-01-31 00:50:17.471][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2025-01-31 00:50:17.473][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:50:17.475][biodb::testThat]
biodb.ERROR[2025-01-31 00:50:17.507][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-01-31 00:50:17.546][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-01-31 00:50:17.579][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-31 00:50:17.582][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-01-31 00:50:17.585][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-01-31 00:50:17.586][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-31 00:50:17.588][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:17.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:17.593][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:17.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:17.597][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:17.599][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.INFO [2025-01-31 00:50:17.643][biodb::testContext]
biodb.INFO [2025-01-31 00:50:17.645][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-31 00:50:17.648][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-01-31 00:50:17.650][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-31 00:50:17.656][biodb::testContext]
biodb.INFO [2025-01-31 00:50:17.661][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-31 00:50:17.664][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-01-31 00:50:17.672][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-31 00:50:17.675][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-31 00:50:17.677][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-31 00:50:17.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:17.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:17.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:17.686][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-31 00:50:17.688][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-31 00:50:17.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:17.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:17.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:17.696][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-31 00:50:17.699][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-31 00:50:17.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:17.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:17.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:17.707][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-31 00:50:17.710][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-31 00:50:17.712][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-31 00:50:17.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:17.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:17.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:17.720][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-31 00:50:17.723][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-31 00:50:17.726][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-31 00:50:17.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:17.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:17.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:17.734][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-31 00:50:17.737][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-31 00:50:17.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:17.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:17.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:17.744][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-31 00:50:17.747][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-31 00:50:17.749][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-31 00:50:17.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:17.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:17.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:17.757][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-31 00:50:17.760][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-31 00:50:17.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:17.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:17.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:17.768][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-31 00:50:17.770][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-31 00:50:17.772][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-31 00:50:17.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:17.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:17.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:17.780][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-31 00:50:17.783][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-31 00:50:17.785][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-31 00:50:17.787][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-31 00:50:17.790][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-31 00:50:17.792][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-31 00:50:17.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:17.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:17.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:17.801][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-31 00:50:17.803][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-31 00:50:17.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:17.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:17.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:17.811][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-31 00:50:17.813][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-31 00:50:17.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:17.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:17.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:17.821][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-31 00:50:17.823][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-31 00:50:17.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:17.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:17.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:17.831][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-31 00:50:17.833][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-31 00:50:17.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:17.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:17.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:17.842][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-31 00:50:17.845][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-31 00:50:17.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:17.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:17.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:17.853][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-31 00:50:17.856][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-31 00:50:17.873][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-31 00:50:17.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:17.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:17.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:17.883][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-31 00:50:17.885][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-31 00:50:17.888][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-31 00:50:17.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:17.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:17.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:17.897][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-31 00:50:17.974][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:17.976][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-31 00:50:17.978][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:17.981][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-31 00:50:17.983][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:17.985][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-31 00:50:17.988][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:17.990][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-31 00:50:17.992][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-31 00:50:17.995][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-31 00:50:17.998][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:18.001][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-31 00:50:18.003][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-31 00:50:18.006][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:18.008][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:18.011][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-31 00:50:18.011][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-31 00:50:18.011][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-31 00:50:18.011][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-31 00:50:18.011][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-31 00:50:18.013][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-31 00:50:18.016][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:18.018][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:18.021][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-31 00:50:18.023][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:18.025][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:18.028][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-31 00:50:18.030][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:18.033][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-31 00:50:18.035][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-31 00:50:18.038][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:18.041][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:18.045][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-31 00:50:18.050][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:18.053][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-31 00:50:18.056][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:18.059][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-31 00:50:18.062][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:18.065][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-31 00:50:18.069][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:18.071][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-31 00:50:18.074][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-31 00:50:18.076][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-31 00:50:18.079][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:18.082][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-31 00:50:18.084][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-31 00:50:18.087][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:18.089][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:18.092][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-31 00:50:18.092][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-31 00:50:18.092][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-31 00:50:18.092][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-31 00:50:18.092][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-31 00:50:18.095][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-31 00:50:18.097][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:18.099][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:18.102][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-31 00:50:18.104][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:18.106][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:18.109][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-31 00:50:18.111][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:18.114][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-31 00:50:18.116][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-31 00:50:18.119][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:18.121][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:18.124][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-31 00:50:18.130][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:18.132][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-31 00:50:18.135][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:18.139][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-31 00:50:18.141][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:18.144][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-31 00:50:18.146][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:18.151][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-31 00:50:18.155][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-31 00:50:18.158][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-31 00:50:18.160][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:18.164][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-31 00:50:18.167][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-31 00:50:18.170][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:18.172][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:18.175][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:18.178][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-31 00:50:18.180][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:18.183][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:18.185][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-31 00:50:18.188][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:18.190][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:18.193][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-31 00:50:18.195][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:18.198][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-31 00:50:18.200][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-31 00:50:18.203][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:18.205][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:18.208][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-31 00:50:18.212][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:18.217][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-31 00:50:18.219][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:18.222][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-31 00:50:18.224][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:18.226][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-31 00:50:18.229][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:18.232][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-31 00:50:18.234][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-31 00:50:18.237][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-31 00:50:18.240][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:18.242][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-31 00:50:18.245][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-31 00:50:18.247][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:18.250][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:18.252][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:18.255][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-31 00:50:18.257][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:18.260][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:18.263][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-31 00:50:18.266][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:18.268][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:18.271][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-31 00:50:18.274][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:18.276][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-31 00:50:18.279][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-31 00:50:18.281][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:18.283][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:18.287][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-31 00:50:18.289][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:18.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:18.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.314][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[2025-01-31 00:50:18.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:18.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.337][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[2025-01-31 00:50:18.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:18.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:18.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.384][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[2025-01-31 00:50:18.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:18.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:18.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.417][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[2025-01-31 00:50:18.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.427][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.DEBUG[2025-01-31 00:50:18.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.438][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.DEBUG[2025-01-31 00:50:18.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:18.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:18.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:18.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.488][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[2025-01-31 00:50:18.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:18.517][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-31 00:50:18.521][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-31 00:50:18.524][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-31 00:50:18.528][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-31 00:50:18.532][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-31 00:50:18.535][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-31 00:50:18.539][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-31 00:50:18.542][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-31 00:50:18.546][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-31 00:50:18.550][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-31 00:50:18.563][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-31 00:50:18.567][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-31 00:50:18.571][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-31 00:50:18.577][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-31 00:50:18.583][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-31 00:50:18.586][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-31 00:50:18.590][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-31 00:50:18.593][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-31 00:50:18.597][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-31 00:50:18.601][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-31 00:50:18.604][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-31 00:50:18.609][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-31 00:50:18.612][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-31 00:50:18.622][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-31 00:50:18.632][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-31 00:50:18.636][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-31 00:50:18.639][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-31 00:50:18.643][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-31 00:50:18.646][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-31 00:50:18.650][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-31 00:50:18.654][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-31 00:50:18.658][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-31 00:50:18.661][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-31 00:50:18.665][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-31 00:50:18.668][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-31 00:50:18.671][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-31 00:50:18.675][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-31 00:50:18.678][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-31 00:50:18.681][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-31 00:50:18.684][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-31 00:50:18.688][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-31 00:50:18.691][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-31 00:50:18.695][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-31 00:50:18.698][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-31 00:50:18.702][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-31 00:50:18.705][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-31 00:50:18.709][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-31 00:50:18.713][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-31 00:50:18.716][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-31 00:50:18.720][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-31 00:50:18.723][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-31 00:50:18.728][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-31 00:50:18.731][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-31 00:50:18.736][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-31 00:50:18.745][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-31 00:50:18.749][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-31 00:50:18.753][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-31 00:50:18.757][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-31 00:50:18.760][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-31 00:50:18.763][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-31 00:50:18.771][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-31 00:50:18.776][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-31 00:50:18.783][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-31 00:50:18.788][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-31 00:50:18.794][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-31 00:50:18.810][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-31 00:50:18.813][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-31 00:50:18.817][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-31 00:50:18.825][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-31 00:50:18.828][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-31 00:50:18.832][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-31 00:50:18.844][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-31 00:50:18.848][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-31 00:50:18.851][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-31 00:50:18.855][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-31 00:50:18.858][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-31 00:50:18.862][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-31 00:50:18.865][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-31 00:50:18.869][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-31 00:50:18.873][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-31 00:50:18.877][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-31 00:50:18.881][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-31 00:50:18.890][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-31 00:50:18.894][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-31 00:50:18.897][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-31 00:50:18.900][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-31 00:50:18.902][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.906][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:18.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:18.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:18.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.922][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[2025-01-31 00:50:18.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:18.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:18.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.937][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[2025-01-31 00:50:18.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:18.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:18.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:18.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:18.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:18.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:18.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:18.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:18.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:18.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:18.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:18.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:18.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:18.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:18.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:19.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:19.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:19.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:19.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:19.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:19.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:19.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:19.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:19.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:19.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:19.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:19.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:19.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:19.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:19.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:19.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:19.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:19.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:19.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:19.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:19.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:19.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:19.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:19.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:19.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:19.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:19.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:19.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:19.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:19.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:19.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:19.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:19.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:19.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:19.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:19.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:19.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:19.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:19.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:19.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:19.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:19.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:19.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:19.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:19.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:19.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:19.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:19.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:19.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:19.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:19.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:19.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:19.115][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[2025-01-31 00:50:19.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:19.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:19.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:19.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:19.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:19.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:19.131][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[2025-01-31 00:50:19.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:19.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:19.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:19.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:19.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:19.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:19.146][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[2025-01-31 00:50:19.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:19.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:19.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:19.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:19.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:19.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:19.161][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[2025-01-31 00:50:19.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:19.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:19.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:19.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:19.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:19.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:19.174][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[2025-01-31 00:50:19.178][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-01-31 00:50:19.181][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-01-31 00:50:19.186][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:19.188][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-31 00:50:19.191][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:19.193][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-31 00:50:19.195][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:19.197][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-31 00:50:19.202][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:19.204][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-01-31 00:50:19.206][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-31 00:50:19.209][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-31 00:50:19.243][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:19.246][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-01-31 00:50:19.249][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-31 00:50:19.253][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-01-31 00:50:19.253][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-01-31 00:50:19.253][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-01-31 00:50:19.253][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-01-31 00:50:19.253][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-01-31 00:50:19.253][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-01-31 00:50:19.253][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-01-31 00:50:19.253][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-01-31 00:50:19.253][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-01-31 00:50:19.253][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-01-31 00:50:19.253][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-01-31 00:50:19.257][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:19.260][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-31 00:50:19.260][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-31 00:50:19.260][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-31 00:50:19.264][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-31 00:50:19.266][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:19.268][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:19.270][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-31 00:50:19.272][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:19.274][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:19.276][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-31 00:50:19.278][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:50:19.278][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-01-31 00:50:19.281][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-31 00:50:19.283][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-31 00:50:19.285][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:19.287][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-01-31 00:50:19.287][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-01-31 00:50:19.290][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-31 00:50:19.293][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-31 00:50:19.297][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-01-31 00:50:19.300][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-31 00:50:19.303][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-31 00:50:19.307][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-31 00:50:19.314][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-01-31 00:50:19.316][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-01-31 00:50:19.319][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-01-31 00:50:19.322][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-01-31 00:50:19.324][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-31 00:50:19.326][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-31 00:50:19.329][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-01-31 00:50:19.331][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-01-31 00:50:19.334][biodb::testThat]
biodb.INFO [2025-01-31 00:50:19.337][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2025-01-31 00:50:19.339][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:50:19.341][biodb::testThat]
biodb.DEBUG[2025-01-31 00:50:19.349][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-01-31 00:50:19.357][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:50:19.359][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:50:19.362][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-01-31 00:50:19.745][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-01-31 00:50:20.258][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:50:20.263][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-01-31 00:50:20.271][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-01-31 00:50:20.280][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:50:20.289][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:50:20.291][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:50:20.295][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-01-31 00:50:20.704][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-01-31 00:50:21.101][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:50:21.105][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-01-31 00:50:21.115][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-01-31 00:50:21.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:21.122][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:21.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:21.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:21.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:21.167][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:21.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:21.175][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[2025-01-31 00:50:21.183][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:50:21.186][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:50:21.190][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-01-31 00:50:21.589][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-01-31 00:50:21.990][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:50:21.994][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-01-31 00:50:22.003][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-01-31 00:50:22.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:22.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:22.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:22.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:22.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:22.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:22.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:22.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:22.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:22.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:22.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:22.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:22.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:22.097][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[2025-01-31 00:50:22.109][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:50:22.117][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-31 00:50:22.120][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-01-31 00:50:22.123][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-31 00:50:22.126][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-01-31 00:50:22.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:22.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:22.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:22.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:22.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:22.150][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:22.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:22.156][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:50:22.164][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-31 00:50:22.167][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-01-31 00:50:22.170][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-31 00:50:22.173][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-01-31 00:50:22.177][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:22.179][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:22.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:22.192][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:22.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:22.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:22.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:22.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:22.203][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:22.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:22.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:22.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:22.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:22.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:22.232][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:50:22.239][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-31 00:50:22.243][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-01-31 00:50:22.246][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-31 00:50:22.249][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-01-31 00:50:22.254][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:22.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:22.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:22.269][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:22.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:22.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:22.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:22.280][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:50:22.288][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-31 00:50:22.291][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-01-31 00:50:22.295][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-31 00:50:22.298][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-01-31 00:50:22.301][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:22.304][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:22.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:22.318][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:22.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:22.322][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:22.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:22.329][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:50:22.343][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:50:22.346][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:50:22.355][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-01-31 00:50:22.750][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-01-31 00:50:23.164][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:50:23.168][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-01-31 00:50:23.179][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-01-31 00:50:23.184][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:23.186][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:23.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:23.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:23.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:23.204][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:23.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-31 00:50:23.222][biodb::testThat]
biodb.INFO [2025-01-31 00:50:23.224][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2025-01-31 00:50:23.227][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:50:23.229][biodb::testThat]
biodb.DEBUG[2025-01-31 00:50:23.236][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[2025-01-31 00:50:23.245][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:50:23.248][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:50:23.254][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-01-31 00:50:23.734][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-01-31 00:50:24.135][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:50:24.140][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-01-31 00:50:24.151][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-01-31 00:50:24.155][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:24.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:24.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:24.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:24.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:24.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:24.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:24.186][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:50:24.194][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:50:24.197][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:50:24.202][private$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[2025-01-31 00:50:24.596][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[2025-01-31 00:50:25.006][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:50:25.011][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-01-31 00:50:25.021][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-01-31 00:50:25.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:25.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:25.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:25.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:25.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:25.047][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-31 00:50:25.061][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-31 00:50:25.065][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-01-31 00:50:25.067][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-01-31 00:50:25.070][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-31 00:50:25.072][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:25.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:25.076][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:25.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:25.081][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.083][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.INFO [2025-01-31 00:50:25.091][biodb::testContext]
biodb.INFO [2025-01-31 00:50:25.094][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-31 00:50:25.097][biodb::testContext] Test context - Test web services
biodb.INFO [2025-01-31 00:50:25.099][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-31 00:50:25.102][biodb::testContext]
biodb.INFO [2025-01-31 00:50:25.106][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-31 00:50:25.110][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-01-31 00:50:25.118][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-31 00:50:25.121][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-31 00:50:25.123][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-31 00:50:25.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.133][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-31 00:50:25.135][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-31 00:50:25.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.144][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-31 00:50:25.146][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-31 00:50:25.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.155][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-31 00:50:25.157][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-31 00:50:25.160][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-31 00:50:25.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.168][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-31 00:50:25.171][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-31 00:50:25.173][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-31 00:50:25.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.183][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-31 00:50:25.185][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-31 00:50:25.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.194][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-31 00:50:25.197][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-31 00:50:25.199][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-31 00:50:25.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.208][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-31 00:50:25.211][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-31 00:50:25.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.220][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-31 00:50:25.223][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-31 00:50:25.225][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-31 00:50:25.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.234][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-31 00:50:25.236][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-31 00:50:25.239][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-31 00:50:25.241][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-31 00:50:25.243][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-31 00:50:25.246][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-31 00:50:25.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.255][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-31 00:50:25.257][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-31 00:50:25.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.266][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-31 00:50:25.268][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-31 00:50:25.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.277][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-31 00:50:25.279][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-31 00:50:25.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.289][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-31 00:50:25.292][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-31 00:50:25.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.333][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-31 00:50:25.336][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-31 00:50:25.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.345][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-31 00:50:25.348][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-31 00:50:25.366][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-31 00:50:25.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.374][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-31 00:50:25.377][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-31 00:50:25.379][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-31 00:50:25.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.388][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-31 00:50:25.391][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:25.394][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-31 00:50:25.396][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:25.398][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-31 00:50:25.401][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:25.403][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-31 00:50:25.405][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:25.407][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-31 00:50:25.409][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-31 00:50:25.412][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-31 00:50:25.414][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:25.417][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-31 00:50:25.420][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-31 00:50:25.422][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:25.424][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:25.426][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-31 00:50:25.426][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-31 00:50:25.426][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-31 00:50:25.426][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-31 00:50:25.426][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-31 00:50:25.429][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-31 00:50:25.431][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:25.433][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:25.435][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-31 00:50:25.438][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:25.440][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:25.442][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-31 00:50:25.444][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:25.446][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-31 00:50:25.449][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-31 00:50:25.451][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:25.453][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:25.456][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-31 00:50:25.460][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:25.462][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-31 00:50:25.465][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:25.467][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-31 00:50:25.470][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:25.472][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-31 00:50:25.474][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:25.476][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-31 00:50:25.478][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-31 00:50:25.481][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-31 00:50:25.483][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:25.486][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-31 00:50:25.488][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-31 00:50:25.490][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:25.492][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:25.495][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-31 00:50:25.495][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-31 00:50:25.495][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-31 00:50:25.495][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-31 00:50:25.495][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-31 00:50:25.498][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-31 00:50:25.500][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:25.501][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:25.503][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-31 00:50:25.506][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:25.508][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:25.510][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-31 00:50:25.512][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:25.513][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-31 00:50:25.515][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-31 00:50:25.517][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:25.520][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:25.522][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-31 00:50:25.525][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:25.527][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-31 00:50:25.529][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:25.531][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-31 00:50:25.533][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:25.535][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-31 00:50:25.537][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:25.540][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-31 00:50:25.542][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-31 00:50:25.544][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-31 00:50:25.547][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:25.549][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-31 00:50:25.551][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-31 00:50:25.554][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:25.556][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:25.559][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:25.561][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-31 00:50:25.563][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:25.564][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:25.566][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-31 00:50:25.567][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:25.568][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:25.570][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-31 00:50:25.571][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:25.572][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-31 00:50:25.574][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-31 00:50:25.576][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:25.578][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:25.581][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-31 00:50:25.586][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:25.588][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-31 00:50:25.590][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:25.593][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-31 00:50:25.595][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:25.597][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-31 00:50:25.599][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:25.601][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-31 00:50:25.604][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-31 00:50:25.606][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-31 00:50:25.608][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:25.611][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-31 00:50:25.613][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-31 00:50:25.616][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:25.618][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:25.620][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:25.623][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-31 00:50:25.625][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:25.627][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:25.629][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-31 00:50:25.632][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:25.634][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:25.636][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-31 00:50:25.638][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:25.640][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-31 00:50:25.642][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-31 00:50:25.644][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:25.647][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:25.650][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-31 00:50:25.652][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:25.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:25.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:25.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:25.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:25.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:25.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.687][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[2025-01-31 00:50:25.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:25.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:25.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:25.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:25.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:25.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:25.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:25.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:25.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:25.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:25.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:25.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:25.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:25.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:25.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:25.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:25.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:25.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:25.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:25.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:25.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.791][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[2025-01-31 00:50:25.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:25.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:25.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:25.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:25.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:25.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:25.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:25.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:25.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:25.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:25.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:25.833][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-31 00:50:25.836][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-31 00:50:25.839][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-31 00:50:25.842][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-31 00:50:25.846][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-31 00:50:25.849][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-31 00:50:25.852][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-31 00:50:25.854][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-31 00:50:25.856][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-31 00:50:25.858][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-31 00:50:25.859][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-31 00:50:25.861][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-31 00:50:25.864][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-31 00:50:25.867][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-31 00:50:25.870][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-31 00:50:25.873][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-31 00:50:25.876][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-31 00:50:25.879][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-31 00:50:25.883][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-31 00:50:25.886][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-31 00:50:25.890][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-31 00:50:25.894][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-31 00:50:25.897][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-31 00:50:25.901][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-31 00:50:25.904][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-31 00:50:25.908][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-31 00:50:25.911][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-31 00:50:25.915][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-31 00:50:25.918][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-31 00:50:25.922][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-31 00:50:25.925][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-31 00:50:25.929][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-31 00:50:25.932][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-31 00:50:25.935][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-31 00:50:25.939][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-31 00:50:25.942][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-31 00:50:25.946][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-31 00:50:25.949][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-31 00:50:25.953][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-31 00:50:25.956][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-31 00:50:25.960][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-31 00:50:25.963][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-31 00:50:25.967][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-31 00:50:25.970][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-31 00:50:25.974][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-31 00:50:25.977][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-31 00:50:25.981][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-31 00:50:25.984][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-31 00:50:25.987][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-31 00:50:25.991][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-31 00:50:25.995][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-31 00:50:25.998][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-31 00:50:26.002][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-31 00:50:26.005][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-31 00:50:26.009][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-31 00:50:26.013][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-31 00:50:26.016][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-31 00:50:26.020][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-31 00:50:26.024][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-31 00:50:26.027][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-31 00:50:26.030][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-31 00:50:26.033][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-31 00:50:26.037][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-31 00:50:26.039][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-31 00:50:26.041][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-31 00:50:26.045][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-31 00:50:26.048][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-31 00:50:26.051][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-31 00:50:26.055][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-31 00:50:26.058][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-31 00:50:26.061][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-31 00:50:26.064][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-31 00:50:26.067][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-31 00:50:26.070][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-31 00:50:26.074][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-31 00:50:26.077][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-31 00:50:26.080][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-31 00:50:26.083][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-31 00:50:26.086][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-31 00:50:26.090][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-31 00:50:26.102][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-31 00:50:26.106][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-31 00:50:26.111][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-31 00:50:26.114][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-31 00:50:26.117][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-31 00:50:26.119][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-31 00:50:26.122][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:26.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:26.126][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:26.127][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[2025-01-31 00:50:26.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:26.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:26.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:26.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:26.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:26.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:26.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:26.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:26.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:26.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:26.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:26.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:26.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:26.155][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[2025-01-31 00:50:26.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:26.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:26.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:26.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:26.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:26.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:26.169][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[2025-01-31 00:50:26.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:26.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:26.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:26.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:26.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:26.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:26.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:26.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:26.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:26.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:26.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:26.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:26.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:26.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:26.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:26.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:26.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:26.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:26.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:26.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:26.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:26.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:26.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:26.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:26.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:26.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:26.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:26.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:26.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:26.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:26.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:26.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:26.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:26.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:26.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:26.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:26.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:26.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:26.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:26.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:26.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:26.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:26.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:26.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:26.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:26.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:26.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:26.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:26.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:26.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:26.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:26.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:26.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:26.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:26.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:26.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:26.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:26.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:26.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:26.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:26.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:26.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:26.297][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[2025-01-31 00:50:26.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:26.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:26.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:26.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:26.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:26.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:26.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:26.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:26.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:26.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:26.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:26.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:26.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:26.324][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[2025-01-31 00:50:26.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:26.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:26.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:26.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:26.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:26.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:26.337][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[2025-01-31 00:50:26.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:26.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:26.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:26.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:26.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:26.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:26.350][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[2025-01-31 00:50:26.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:26.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:26.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:26.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:26.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:26.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:26.364][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[2025-01-31 00:50:26.368][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-01-31 00:50:26.372][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-01-31 00:50:26.377][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:26.379][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-31 00:50:26.382][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:26.384][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-31 00:50:26.386][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:26.389][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-31 00:50:26.391][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:26.393][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-01-31 00:50:26.395][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-31 00:50:26.398][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-31 00:50:26.400][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:26.403][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-01-31 00:50:26.405][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-31 00:50:26.407][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-01-31 00:50:26.407][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-01-31 00:50:26.407][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-01-31 00:50:26.407][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-01-31 00:50:26.407][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-01-31 00:50:26.407][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-01-31 00:50:26.407][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-01-31 00:50:26.407][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-01-31 00:50:26.407][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-01-31 00:50:26.407][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-01-31 00:50:26.407][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-01-31 00:50:26.410][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:26.413][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-31 00:50:26.413][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-31 00:50:26.413][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-31 00:50:26.415][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-31 00:50:26.418][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:26.420][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:26.422][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-31 00:50:26.425][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:26.427][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:26.429][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-31 00:50:26.431][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:50:26.431][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-01-31 00:50:26.433][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-31 00:50:26.436][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-31 00:50:26.438][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:26.440][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-01-31 00:50:26.440][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-01-31 00:50:26.444][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-31 00:50:26.447][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-31 00:50:26.451][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-01-31 00:50:26.455][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-31 00:50:26.458][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-31 00:50:26.462][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-31 00:50:26.470][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-01-31 00:50:26.473][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-01-31 00:50:26.475][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-01-31 00:50:26.478][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-01-31 00:50:26.481][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-31 00:50:26.484][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-31 00:50:26.486][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-01-31 00:50:26.489][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-01-31 00:50:26.492][biodb::testThat]
biodb.INFO [2025-01-31 00:50:26.494][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-01-31 00:50:26.496][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:50:26.498][biodb::testThat]
biodb.DEBUG[2025-01-31 00:50:26.505][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-01-31 00:50:26.513][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-31 00:50:26.516][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-01-31 00:50:26.519][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-31 00:50:26.522][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-01-31 00:50:26.530][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[2025-01-31 00:50:26.537][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:50:26.539][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:50:26.543][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-01-31 00:50:26.943][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-01-31 00:50:27.342][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:50:27.347][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-01-31 00:50:27.356][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-01-31 00:50:27.375][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-31 00:50:27.378][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-01-31 00:50:27.380][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-01-31 00:50:27.382][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-31 00:50:27.384][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:27.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:27.388][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:27.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:27.393][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-31 00:50:27.402][biodb::testContext]
biodb.INFO [2025-01-31 00:50:27.404][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-31 00:50:27.406][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-01-31 00:50:27.408][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-31 00:50:27.411][biodb::testContext]
biodb.INFO [2025-01-31 00:50:27.415][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-31 00:50:27.419][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-01-31 00:50:27.426][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-31 00:50:27.428][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-31 00:50:27.431][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-31 00:50:27.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:27.439][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-31 00:50:27.442][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-31 00:50:27.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:27.450][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-31 00:50:27.451][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-31 00:50:27.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:27.459][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-31 00:50:27.461][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-31 00:50:27.464][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-31 00:50:27.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:27.470][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-31 00:50:27.472][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-31 00:50:27.475][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-31 00:50:27.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:27.483][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-31 00:50:27.485][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-31 00:50:27.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:27.494][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-31 00:50:27.497][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-31 00:50:27.499][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-31 00:50:27.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:27.508][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-31 00:50:27.511][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-31 00:50:27.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:27.520][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-31 00:50:27.522][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-31 00:50:27.525][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-31 00:50:27.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.531][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[2025-01-31 00:50:27.533][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-31 00:50:27.536][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-31 00:50:27.537][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-31 00:50:27.539][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-31 00:50:27.542][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-31 00:50:27.544][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-31 00:50:27.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:27.552][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-31 00:50:27.555][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-31 00:50:27.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:27.562][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-31 00:50:27.564][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-31 00:50:27.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:27.570][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-31 00:50:27.573][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-31 00:50:27.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:27.580][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-31 00:50:27.583][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-31 00:50:27.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:27.591][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-31 00:50:27.593][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-31 00:50:27.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:27.601][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-31 00:50:27.603][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-31 00:50:27.620][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-31 00:50:27.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:27.628][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-31 00:50:27.630][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-31 00:50:27.632][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-31 00:50:27.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:27.639][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-31 00:50:27.642][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:27.643][self$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[2025-01-31 00:50:27.645][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:27.647][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-31 00:50:27.649][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:27.652][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-31 00:50:27.654][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:27.656][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-31 00:50:27.659][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-31 00:50:27.662][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-31 00:50:27.664][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:27.682][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-31 00:50:27.684][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-31 00:50:27.687][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:27.690][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:27.692][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-31 00:50:27.692][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-31 00:50:27.692][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-31 00:50:27.692][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-31 00:50:27.692][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-31 00:50:27.695][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-31 00:50:27.697][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:27.699][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:27.701][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-31 00:50:27.704][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:27.706][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:27.708][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-31 00:50:27.710][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:27.713][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-31 00:50:27.715][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-31 00:50:27.717][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:27.719][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:27.722][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-31 00:50:27.726][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:27.728][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-31 00:50:27.730][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:27.733][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-31 00:50:27.735][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:27.737][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-31 00:50:27.739][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:27.741][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-31 00:50:27.743][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-31 00:50:27.745][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-31 00:50:27.748][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:27.750][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-31 00:50:27.752][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-31 00:50:27.754][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:27.756][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:27.758][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-31 00:50:27.758][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-31 00:50:27.758][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-31 00:50:27.758][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-31 00:50:27.758][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-31 00:50:27.761][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-31 00:50:27.763][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:27.765][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:27.767][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-31 00:50:27.769][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:27.771][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:27.774][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-31 00:50:27.776][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:27.778][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-31 00:50:27.780][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-31 00:50:27.783][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:27.785][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:27.787][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-31 00:50:27.791][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:27.793][self$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[2025-01-31 00:50:27.795][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:27.798][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-31 00:50:27.800][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:27.802][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-31 00:50:27.804][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:27.807][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-31 00:50:27.809][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-31 00:50:27.811][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-31 00:50:27.813][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:27.816][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-31 00:50:27.818][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-31 00:50:27.820][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:27.822][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:27.825][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:27.827][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-31 00:50:27.830][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:27.832][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:27.834][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-31 00:50:27.837][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:27.839][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:27.841][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-31 00:50:27.844][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:27.846][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-31 00:50:27.848][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-31 00:50:27.850][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:27.852][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:27.855][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-31 00:50:27.860][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:27.862][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-31 00:50:27.865][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:27.867][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-31 00:50:27.869][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:27.872][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-31 00:50:27.874][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:27.877][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-31 00:50:27.880][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-31 00:50:27.882][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-31 00:50:27.885][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:27.887][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-31 00:50:27.890][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-31 00:50:27.892][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:27.895][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:27.897][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:27.900][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-31 00:50:27.903][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:27.905][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:27.907][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-31 00:50:27.910][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:27.912][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:27.915][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-31 00:50:27.917][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:27.920][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-31 00:50:27.922][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-31 00:50:27.925][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:27.927][self$setPropertyValue]
biodb.DEBUG[2025-01-31 00:50:27.930][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-31 00:50:27.932][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.934][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[2025-01-31 00:50:27.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:27.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:27.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.945][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[2025-01-31 00:50:27.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:27.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:27.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:27.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:27.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:27.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:27.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:27.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:27.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:27.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:27.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:27.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:27.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:27.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:27.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:27.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:27.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:28.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:28.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:28.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:28.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:28.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.059][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[2025-01-31 00:50:28.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.069][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[2025-01-31 00:50:28.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.080][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[2025-01-31 00:50:28.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:28.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:28.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.113][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[2025-01-31 00:50:28.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.124][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[2025-01-31 00:50:28.127][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-31 00:50:28.131][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-31 00:50:28.135][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-31 00:50:28.138][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-31 00:50:28.142][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-31 00:50:28.146][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-31 00:50:28.150][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-31 00:50:28.153][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-31 00:50:28.157][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-31 00:50:28.160][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-31 00:50:28.163][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-31 00:50:28.167][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-31 00:50:28.170][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-31 00:50:28.173][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-31 00:50:28.177][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-31 00:50:28.181][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-31 00:50:28.184][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-31 00:50:28.188][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-31 00:50:28.191][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-31 00:50:28.195][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-31 00:50:28.198][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-31 00:50:28.202][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-31 00:50:28.205][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-31 00:50:28.209][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-31 00:50:28.212][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-31 00:50:28.215][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-31 00:50:28.219][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-31 00:50:28.222][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-31 00:50:28.226][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-31 00:50:28.229][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-31 00:50:28.233][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-31 00:50:28.236][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-31 00:50:28.239][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-31 00:50:28.243][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-31 00:50:28.246][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-31 00:50:28.249][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-31 00:50:28.253][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-31 00:50:28.256][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-31 00:50:28.260][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-31 00:50:28.262][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-31 00:50:28.265][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-31 00:50:28.269][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-31 00:50:28.271][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-31 00:50:28.275][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-31 00:50:28.278][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-31 00:50:28.281][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-31 00:50:28.285][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-31 00:50:28.288][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-31 00:50:28.292][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-31 00:50:28.295][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-31 00:50:28.297][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-31 00:50:28.299][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-31 00:50:28.301][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-31 00:50:28.304][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-31 00:50:28.307][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-31 00:50:28.311][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-31 00:50:28.313][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-31 00:50:28.315][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-31 00:50:28.317][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-31 00:50:28.319][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-31 00:50:28.322][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-31 00:50:28.325][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-31 00:50:28.329][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-31 00:50:28.331][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-31 00:50:28.334][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-31 00:50:28.336][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-31 00:50:28.339][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-31 00:50:28.341][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-31 00:50:28.344][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-31 00:50:28.347][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-31 00:50:28.350][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-31 00:50:28.354][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-31 00:50:28.357][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-31 00:50:28.361][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-31 00:50:28.365][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-31 00:50:28.368][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-31 00:50:28.372][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-31 00:50:28.375][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-31 00:50:28.379][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-31 00:50:28.382][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-31 00:50:28.386][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-31 00:50:28.389][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-31 00:50:28.393][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-31 00:50:28.397][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-31 00:50:28.400][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-31 00:50:28.403][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-31 00:50:28.405][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.409][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:28.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:28.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:28.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:28.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:28.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:28.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.438][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.DEBUG[2025-01-31 00:50:28.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:28.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:28.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:28.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:28.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:28.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:28.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:28.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:28.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:28.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:28.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:28.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:28.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:28.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:28.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.518][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[2025-01-31 00:50:28.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:28.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:28.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:28.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:28.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:28.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.548][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[2025-01-31 00:50:28.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:28.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:28.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:28.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:28.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:28.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.576][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[2025-01-31 00:50:28.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:28.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:28.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:28.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:28.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:28.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:28.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:28.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:28.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:28.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:28.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:28.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.628][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[2025-01-31 00:50:28.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:28.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:28.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.644][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[2025-01-31 00:50:28.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-31 00:50:28.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:28.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:28.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:28.666][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-01-31 00:50:28.670][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-01-31 00:50:28.676][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:28.678][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-31 00:50:28.680][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:28.682][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-31 00:50:28.684][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:28.686][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-31 00:50:28.689][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:28.691][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-01-31 00:50:28.694][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-31 00:50:28.696][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-31 00:50:28.699][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:28.701][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-01-31 00:50:28.703][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-31 00:50:28.706][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-01-31 00:50:28.706][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-01-31 00:50:28.706][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-01-31 00:50:28.706][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-01-31 00:50:28.706][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-01-31 00:50:28.706][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-01-31 00:50:28.706][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-01-31 00:50:28.706][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-01-31 00:50:28.706][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-01-31 00:50:28.706][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-01-31 00:50:28.706][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-01-31 00:50:28.709][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-31 00:50:28.712][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-31 00:50:28.712][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-31 00:50:28.712][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-31 00:50:28.715][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-31 00:50:28.717][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:28.719][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:28.722][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-31 00:50:28.724][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-31 00:50:28.727][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-31 00:50:28.729][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-31 00:50:28.732][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:50:28.732][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-01-31 00:50:28.734][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-31 00:50:28.736][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-31 00:50:28.738][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-31 00:50:28.741][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-01-31 00:50:28.741][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-01-31 00:50:28.744][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-31 00:50:28.748][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-31 00:50:28.752][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-01-31 00:50:28.755][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-31 00:50:28.759][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-31 00:50:28.763][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-31 00:50:28.770][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-01-31 00:50:28.773][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-01-31 00:50:28.775][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-01-31 00:50:28.778][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-01-31 00:50:28.781][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-31 00:50:28.783][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-31 00:50:28.787][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-01-31 00:50:28.789][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-01-31 00:50:28.792][biodb::testThat]
biodb.INFO [2025-01-31 00:50:28.794][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-01-31 00:50:28.796][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-31 00:50:28.798][biodb::testThat]
biodb.DEBUG[2025-01-31 00:50:28.805][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-01-31 00:50:28.813][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-31 00:50:28.816][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-01-31 00:50:28.819][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-31 00:50:28.822][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-01-31 00:50:28.830][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-31 00:50:28.838][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-31 00:50:28.840][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-01-31 00:50:28.843][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-31 00:50:28.846][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-01-31 00:50:28.854][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-01-31 00:50:28.855][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-31 00:50:28.858][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-01-31 00:50:28.861][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-31 00:50:28.864][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-31 00:50:28.866][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-31 00:50:28.869][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-31 00:50:28.871][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-31 00:50:28.874][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-31 00:50:28.879][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:28.881][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:28.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:28.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:28.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:28.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:28.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-31 00:50:28.903][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-01-31 00:50:28.910][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-31 00:50:28.912][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-31 00:50:28.915][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-01-31 00:50:33.537][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-01-31 00:50:34.208][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-31 00:50:34.213][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-01-31 00:50:34.221][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-01-31 00:50:34.227][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-01-31 00:50:34.231][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-31 00:50:34.234][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-31 00:50:34.236][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-31 00:50:34.239][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-31 00:50:34.241][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:34.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:34.253][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:34.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:34.257][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:34.260][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.TRACE[2025-01-31 00:50:34.268][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:34.269][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:34.271][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.273][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:34.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:34.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.283][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:50:34.285][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:50:34.288][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.290][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.350][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-31 00:50:34.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-31 00:50:34.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.359][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:50:34.361][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:50:34.364][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.366][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.369][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-31 00:50:34.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-31 00:50:34.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.379][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-31 00:50:34.381][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-31 00:50:34.384][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.386][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.389][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-31 00:50:34.391][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-31 00:50:34.393][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.395][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.398][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:50:34.401][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:50:34.403][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.404][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.406][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:50:34.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-31 00:50:34.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.415][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:50:34.417][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:34.418][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.419][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.421][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-31 00:50:34.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-31 00:50:34.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.429][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:34.431][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:34.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.433][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:34.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-31 00:50:34.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.441][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:50:34.442][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:50:34.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.445][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.448][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-31 00:50:34.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-31 00:50:34.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.457][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:50:34.460][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:50:34.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.465][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.468][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-31 00:50:34.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-31 00:50:34.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.478][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:50:34.481][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:50:34.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.485][ef$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.489][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-31 00:50:34.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-31 00:50:34.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:34.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:34.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:34.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:34.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:34.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:34.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-31 00:50:34.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-31 00:50:34.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:34.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:34.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:34.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:34.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:34.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:34.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:34.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:34.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:34.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:34.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-31 00:50:34.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-31 00:50:34.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-31 00:50:34.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-31 00:50:34.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-31 00:50:34.681][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-01-31 00:50:34.693][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-31 00:50:34.695][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-01-31 00:50:34.698][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-01-31 00:50:34.700][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-31 00:50:34.702][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-31 00:50:34.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-31 00:50:34.706][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-31 00:50:34.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-31 00:50:34.710][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-31 00:50:34.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
> 
> proc.time()
   user  system elapsed 
 44.647   2.026  96.123

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn4.7161.2546.908
ChebiEntry0.7870.0250.843